t/data/phmmer.out

   1 # phmmer :: search a protein sequence against a protein database
   2 # HMMER 3.1b1 (May 2013); http://hmmer.org/
   3 # Copyright (C) 2013 Howard Hughes Medical Institute.
   4 # Freely distributed under the GNU General Public License (GPLv3).
   5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   6 # query sequence file:             /tmp/task-hmmsearch-TCHn9R/ZRkI2xwebU
   7 # target sequence database:        /cath/data/v4_0_0/release_data/CathDomainSeqs.COMBS
   8 # output directed to file:         /tmp/phmmer.out
   9 # sequence reporting threshold:    E-value <= 0.01
  10 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  11
  12 Query:       A0R3R7  [L=762]
  13 Scores for complete sequences (score includes all domains):
  14    --- full sequence ---   --- best 1 domain ---    -#dom-
  15     E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
  16     ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
  17     2.1e-55  191.8   3.7    2.3e-55  191.7   3.7    1.0  1  cath|4_0_0|1vs0A03/639-759
  18     2.1e-55  191.8   3.7    2.3e-55  191.7   3.7    1.0  1  cath|4_0_0|1vs0B03/639-759
  19     1.9e-46  162.2   0.2    2.1e-46  162.1   0.2    1.0  1  cath|4_0_0|1vs0A02/484-593
  20     1.9e-46  162.2   0.2    2.1e-46  162.1   0.2    1.0  1  cath|4_0_0|1vs0B02/484-593
  21     5.8e-17   64.7   1.4    7.1e-10   41.3   0.1    2.0  2  cath|4_0_0|1vs0A01/453-483_594-638
  22     5.8e-17   64.7   1.4    7.1e-10   41.3   0.1    2.0  2  cath|4_0_0|1vs0B01/453-483_594-638
  23     6.4e-07   31.5   0.1    8.1e-07   31.2   0.1    1.0  1  cath|4_0_0|2cfmA03/422-561
  24     0.00065   21.6   0.0    0.00069   21.5   0.0    1.0  1  cath|4_0_0|1x9nA03/571-696
  25
  26
  27 Domain annotation for each sequence (and alignments):
  28 >> cath|4_0_0|1vs0A03/639-759
  29    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
  30  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
  31    1 !  191.7   3.7   7.9e-60   2.3e-55     642     761 ..       1     120 [.       1     121 [] 0.99
  32
  33   Alignments for each domain:
  34   == domain 1  score: 191.7 bits;  conditional E-value: 7.9e-60
  35                       A0R3R7 642 wntqevviggwrqgeggrssgigalvlgipgpeglqfvgrvgtgftekelsklkdmlkplhtdespfnaplpkvdargvtfvr 724
  36                                  wntqevviggwr geggrssg+g+l+ gipgp glqf grvgtg++e+el+ lk+ l plhtdespf+ plp  da+g+t+v+
  37   cath|4_0_0|1vs0A03/639-759   1 WNTQEVVIGGWRAGEGGRSSGVGSLLXGIPGPGGLQFAGRVGTGLSERELANLKEXLAPLHTDESPFDVPLPARDAKGITYVK 83
  38                                  *********************************************************************************** PP
  39
  40                       A0R3R7 725 pelvgevrysertsdgrlrqpswrglrpdktpdevvw 761
  41                                  p lv+evryse t +grlrq swrglrpdk p evv
  42   cath|4_0_0|1vs0A03/639-759  84 PALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEVVR 120
  43                                  ***********************************96 PP
  44
  45 >> cath|4_0_0|1vs0B03/639-759
  46    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
  47  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
  48    1 !  191.7   3.7   7.9e-60   2.3e-55     642     761 ..       1     120 [.       1     121 [] 0.99
  49
  50   Alignments for each domain:
  51   == domain 1  score: 191.7 bits;  conditional E-value: 7.9e-60
  52                       A0R3R7 642 wntqevviggwrqgeggrssgigalvlgipgpeglqfvgrvgtgftekelsklkdmlkplhtdespfnaplpkvdargvtfvr 724
  53                                  wntqevviggwr geggrssg+g+l+ gipgp glqf grvgtg++e+el+ lk+ l plhtdespf+ plp  da+g+t+v+
  54   cath|4_0_0|1vs0B03/639-759   1 WNTQEVVIGGWRAGEGGRSSGVGSLLXGIPGPGGLQFAGRVGTGLSERELANLKEXLAPLHTDESPFDVPLPARDAKGITYVK 83
  55                                  *********************************************************************************** PP
  56
  57                       A0R3R7 725 pelvgevrysertsdgrlrqpswrglrpdktpdevvw 761
  58                                  p lv+evryse t +grlrq swrglrpdk p evv
  59   cath|4_0_0|1vs0B03/639-759  84 PALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEVVR 120
  60                                  ***********************************96 PP
  61
  62 >> cath|4_0_0|1vs0A02/484-593
  63    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
  64  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
  65    1 !  162.1   0.2     7e-51   2.1e-46     487     596 ..       1     110 []       1     110 [] 0.99
  66
  67   Alignments for each domain:
  68   == domain 1  score: 162.1 bits;  conditional E-value: 7e-51
  69                       A0R3R7 487 gyrviidadhgqlqirsrtgrevtgeypqfkalaadlaehhvvldgeavaldesgvpsfgqmqnrarstrvefwafdilwldg 569
  70                                  gyr++++adhg +++rsr+gr+vt+eypq++ala dla+hhvvldgeav ld sgvpsf+q qnr r trvefwafd+l+ldg
  71   cath|4_0_0|1vs0A02/484-593   1 GYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVPSFSQXQNRGRDTRVEFWAFDLLYLDG 83
  72                                  8********************************************************************************** PP
  73
  74                       A0R3R7 570 rsllrakysdrrkilealadggglivp 596
  75                                  r+ll  +y drrk+le la++ +l vp
  76   cath|4_0_0|1vs0A02/484-593  84 RALLGTRYQDRRKLLETLANATSLTVP 110
  77                                  *********************999998 PP
  78
  79 >> cath|4_0_0|1vs0B02/484-593
  80    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
  81  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
  82    1 !  162.1   0.2     7e-51   2.1e-46     487     596 ..       1     110 []       1     110 [] 0.99
  83
  84   Alignments for each domain:
  85   == domain 1  score: 162.1 bits;  conditional E-value: 7e-51
  86                       A0R3R7 487 gyrviidadhgqlqirsrtgrevtgeypqfkalaadlaehhvvldgeavaldesgvpsfgqmqnrarstrvefwafdilwldg 569
  87                                  gyr++++adhg +++rsr+gr+vt+eypq++ala dla+hhvvldgeav ld sgvpsf+q qnr r trvefwafd+l+ldg
  88   cath|4_0_0|1vs0B02/484-593   1 GYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVPSFSQXQNRGRDTRVEFWAFDLLYLDG 83
  89                                  8********************************************************************************** PP
  90
  91                       A0R3R7 570 rsllrakysdrrkilealadggglivp 596
  92                                  r+ll  +y drrk+le la++ +l vp
  93   cath|4_0_0|1vs0B02/484-593  84 RALLGTRYQDRRKLLETLANATSLTVP 110
  94                                  *********************999998 PP
  95
  96 >> cath|4_0_0|1vs0A01/453-483_594-638
  97    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
  98  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
  99    1 !   24.0   0.1   4.2e-09   0.00012     459     487 ..       7      35 ..       4      37 .. 0.93
 100    2 !   41.3   0.1   2.4e-14   7.1e-10     598     640 ..      36      78 ..      34      79 .] 0.96
 101
 102   Alignments for each domain:
 103   == domain 1  score: 24.0 bits;  conditional E-value: 4.2e-09
 104                               A0R3R7 459 edfapmlategsvakykakqwafegkwdg 487
 105                                          +++ap lat g+va  ka qwafeg wd
 106   cath|4_0_0|1vs0A01/453-483_594-638   7 DNLAPXLATHGTVAGLKASQWAFEGXWDE 35
 107                                          578************************95 PP
 108
 109   == domain 2  score: 41.3 bits;  conditional E-value: 2.4e-14
 110                               A0R3R7 598 qlpgdgpeamehvrkkrfegvvakkwdstyqpgrrssswikdk 640
 111                                           lpgdg +a+   rk  +egv+ak+ ds yqpgrr +sw+kdk
 112   cath|4_0_0|1vs0A01/453-483_594-638  36 LLPGDGAQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDK 78
 113                                          69****************************************8 PP
 114
 115 >> cath|4_0_0|1vs0B01/453-483_594-638
 116    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 117  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
 118    1 !   24.0   0.1   4.2e-09   0.00012     459     487 ..       7      35 ..       4      37 .. 0.93
 119    2 !   41.3   0.1   2.4e-14   7.1e-10     598     640 ..      36      78 ..      34      79 .] 0.96
 120
 121   Alignments for each domain:
 122   == domain 1  score: 24.0 bits;  conditional E-value: 4.2e-09
 123                               A0R3R7 459 edfapmlategsvakykakqwafegkwdg 487
 124                                          +++ap lat g+va  ka qwafeg wd
 125   cath|4_0_0|1vs0B01/453-483_594-638   7 DNLAPXLATHGTVAGLKASQWAFEGXWDE 35
 126                                          578************************95 PP
 127
 128   == domain 2  score: 41.3 bits;  conditional E-value: 2.4e-14
 129                               A0R3R7 598 qlpgdgpeamehvrkkrfegvvakkwdstyqpgrrssswikdk 640
 130                                           lpgdg +a+   rk  +egv+ak+ ds yqpgrr +sw+kdk
 131   cath|4_0_0|1vs0B01/453-483_594-638  36 LLPGDGAQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDK 78
 132                                          69****************************************8 PP
 133
 134 >> cath|4_0_0|2cfmA03/422-561
 135    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 136  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
 137    1 !   31.2   0.1   2.7e-11   8.1e-07     646     758 ..       8     117 ..       2     120 .. 0.80
 138
 139   Alignments for each domain:
 140   == domain 1  score: 31.2 bits;  conditional E-value: 2.7e-11
 141                       A0R3R7 646 evviggwrqgeggrssgigalvlgipgpeglqf..vgrvgtgftekelsklkdmlkplhtdespfnapl.pkvdargvtfvrp 725
 142                                  ++vi g + geg r+  +g+++lg   pe  +f  vg+vg+gft+ +l ++   lkpl   e      l pkv    vt+
 143   cath|4_0_0|2cfmA03/422-561   8 DLVIIGAEWGEGRRAHLFGSFILGAYDPETGEFleVGKVGSGFTDDDLVEFTKXLKPLIIKEEGKRVWLqPKVV-IEVTYQ-- 87
 144                                  456667789********************9888667**********************9988877776636664.446663.. PP
 145
 146                       A0R3R7 726 elvgevrysertsdgrlrqpswrglrpdktpde 758
 147                                  e+    +y    s   lr p + +lr dk p++
 148   cath|4_0_0|2cfmA03/422-561  88 EIQKSPKY---RSGFALRFPRFVALRDDKGPED 117
 149                                  44444444...355689************9987 PP
 150
 151 >> cath|4_0_0|1x9nA03/571-696
 152    #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 153  ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
 154    1 !   21.5   0.0   2.3e-08   0.00069     494     585 ..       9     113 ..       1     124 [. 0.74
 155
 156   Alignments for each domain:
 157   == domain 1  score: 21.5 bits;  conditional E-value: 2.3e-08
 158                       A0R3R7 494 adhgqlqirsrtgrevtgeypqfkalaadlae...hhvvldgeavalde..sgvpsfgqmqnrars........trvefwafd 563
 159                                   + g+++i sr  ++ tg+yp + +    +        +ld eava d     +  f  +  r r          +v ++afd
 160   cath|4_0_0|1x9nA03/571-696   9 LEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLpsvTSFILDTEAVAWDRekKQIQPFQVLTTRKRKevdaseiqVQVCLYAFD 91
 161                                  36799*****************98776665430114679*******9962256889998888877422222211345589*** PP
 162
 163                       A0R3R7 564 ilwldgrsllrakysdrrkile 585
 164                                  +++l+g+sl+r   s rr++l
 165   cath|4_0_0|1x9nA03/571-696  92 LIYLNGESLVREPLSRRRQLLR 113
 166                                  ******************9985 PP
 167
 168
 169
 170 Internal pipeline statistics summary:
 171 -------------------------------------
 172 Query model(s):                              1  (762 nodes)
 173 Target sequences:                       235858  (38973128 residues searched)
 174 Passed MSV filter:                      6997  (0.0296662); expected 4717.2 (0.02)
 175 Passed bias filter:                     6066  (0.0257189); expected 4717.2 (0.02)
 176 Passed Vit filter:                       317  (0.00134403); expected 235.9 (0.001)
 177 Passed Fwd filter:                         9  (3.81586e-05); expected 2.4 (1e-05)
 178 Initial search space (Z):             235858  [actual number of targets]
 179 Domain search space  (domZ):               8  [number of targets reported over threshold]
 180 # CPU time: 4.10u 0.03s 00:00:04.13 Elapsed: 00:00:00.62
 181 # Mc/sec: 47899.23
 182 //
 183 [ok]