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# hmmscan :: search sequence(s) against a profile database
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# HMMER 3.0 (March 2010); http://hmmer.org/
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# Copyright (C) 2010 Howard Hughes Medical Institute.
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# Freely distributed under the GNU General Public License (GPLv3).
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# query sequence file: BA000019.orf1.fasta
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# target HMM database: /data/biodata/HMMerDB/Pfam.hmm
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Query: BA000019.orf1 [L=198]
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Scores for complete sequence (score includes all domains):
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--- full sequence --- --- best 1 domain --- -#dom-
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E-value score bias E-value score bias exp N Model Description
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------- ------ ----- ------- ------ ----- ---- -- -------- -----------
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6e-30 105.2 0.3 6.7e-30 105.0 0.2 1.0 1 Peripla_BP_2 Periplasmic binding protein
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------ inclusion threshold ------
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0.036 14.7 0.0 0.09 13.4 0.0 1.7 1 DUF2726 Protein of unknown function (DUF2726)
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0.039 14.1 0.3 0.049 13.8 0.2 1.1 1 Pfam-B_1590
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0.22 12.5 0.0 0.33 12.0 0.0 1.3 1 Pfam-B_6580
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0.25 12.1 0.2 0.37 11.5 0.2 1.2 1 Calpain_III Calpain large subunit, domain III
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0.42 11.5 1.2 1.7 9.5 0.1 2.3 3 MHCassoc_trimer Class II MHC-associated invariant chain trim
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1.2 9.2 2.2 1.3 9.1 1.5 1.1 1 DUF3498 Domain of unknown function (DUF3498)
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Domain annotation for each model (and alignments):
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>> Peripla_BP_2 Periplasmic binding protein
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ! 105.0 0.2 1.5e-33 6.7e-30 59 236 .. 2 173 .. 1 175 [. 0.93
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Alignments for each domain:
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== domain 1 score: 105.0 bits; conditional E-value: 1.5e-33
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Peripla_BP_2 59 lkPDlvivsafgalvseieellelgipvvavessstaeslleqirllgellgeedeaeelvaelesridavkaridsl.kpktvlvfgyadegikv 153
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lkPDl+i+ +++ ++i+++l++ +p+v v+ s+ s+++ +r ++++l+ee++++ + +++++ri+++++r + ++ +v+v+g+++ +ik+
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BA000019.orf1 2 LKPDLIIGREYQ---KNIYNQLSNFAPTVLVDWGSF-TSFQDNFRYIAQVLNEEEQGKLVLQQYQKRIRDLQDRMGERlQKIEVSVIGFSGQSIKS 93
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8***********...********************9.*****************************************999999999999997777 PP
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Peripla_BP_2 154 vfgsgswvgdlldaaggeni.iaeakgseseeisaEqilaadpdviivsgrgedtktgveelkenplwaelpAvkngrvyllds 236
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++ + ++++ld+ag++ i i++++++ + eis+E+++++d+dv++v k+ + ++nplw +l+Avk+++vy++++
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BA000019.orf1 94 LNR-DAVFNQVLDDAGIKRIsIQKNQQERYLEISIENLNKYDADVLFVINE---SKEQLYPDLKNPLWHHLRAVKKQQVYVVNQ 173
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776.5678999999****99777777*************************...77777777899***************9976 PP
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>> DUF2726 Protein of unknown function (DUF2726)
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 13.4 0.0 2e-05 0.09 79 112 .. 86 119 .. 79 130 .. 0.75
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Alignments for each domain:
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== domain 1 score: 13.4 bits; conditional E-value: 2e-05
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DUF2726 79 ashkqgkaekrDalkeealekAgipllrvkakks 112
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+s ++ k +rDa+++++l+ Agi+ + +++ ++
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BA000019.orf1 86 FSGQSIKSLNRDAVFNQVLDDAGIKRISIQKNQQ 119
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4555777999****************99954433 PP
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 13.8 0.2 1.1e-05 0.049 6 102 .. 78 169 .. 74 195 .. 0.75
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Alignments for each domain:
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== domain 1 score: 13.8 bits; conditional E-value: 1.1e-05
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Pfam-B_1590 6 risafinlfiGqsvsrktivnail.slleqkGflkrswnkinlpctyvnlsieriskfdflpilskikgkeisyklyGeteWqtidklLlnvnkhk 100
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+i + f Gqs++ + +a++ +l++ G + s +k n y+++sie+++k+d ++ + ke +y + + W+++ v+k++
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BA000019.orf1 78 KIEVSVIGFSGQSIKSLNR-DAVFnQVLDDAGIKRISIQK-NQQERYLEISIENLNKYDADVLFVINESKEQLYPDLKNPLWHHLR----AVKKQQ 167
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5666666789999876554.34441578999999999988.56789*************98888888899****999999997654....444444 PP
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Pfam-B_1590 101 af 102
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BA000019.orf1 168 VY 169
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 12.0 0.0 7.2e-05 0.33 36 89 .. 70 124 .. 61 139 .. 0.83
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Alignments for each domain:
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== domain 1 score: 12.0 bits; conditional E-value: 7.2e-05
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Pfam-B_6580 36 ewLedrlataaaAalvldalqseelpr.alqrelLeaigakavvlrkdqtrrlla 89
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+++ +rl+++++ + + + l+r a+ +++L+ +g+k + ++k+q+ r l
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BA000019.orf1 70 DRMGERLQKIEVSVIGFSGQSIKSLNRdAVFNQVLDDAGIKRISIQKNQQERYLE 124
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5677889999999999999988888862699******************999764 PP
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>> Calpain_III Calpain large subunit, domain III
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 11.5 0.2 8.1e-05 0.37 25 91 .. 35 102 .. 31 129 .. 0.75
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Alignments for each domain:
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== domain 1 score: 11.5 bits; conditional E-value: 8.1e-05
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Calpain_III 25 etfltNPqfrlslkepddedctvliaLmqknrrkkrkk.geenltigfavykv.kkkekeldkeffkkn 91
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+f +N + ++ +++++ +++++ +qk+ r ++ ge++ i+++v+ +++ k+l+++++ ++
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BA000019.orf1 35 TSFQDNFRYIAQVLNEEEQ-GKLVLQQYQKRIRDLQDRmGERLQKIEVSVIGFsGQSIKSLNRDAVFNQ 102
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48999**********9987.7999999999988776655888888999998887777788888766555 PP
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>> MHCassoc_trimer Class II MHC-associated invariant chain trimerisation domain
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? -3.5 0.0 4.3 2e+04 41 49 .. 29 37 .. 27 41 .. 0.78
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2 ? 0.1 0.0 0.35 1.6e+03 4 36 .. 51 81 .. 49 96 .. 0.74
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3 ? 9.5 0.1 0.00038 1.7 9 43 .. 139 176 .. 131 178 .. 0.73
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Alignments for each domain:
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== domain 1 score: -3.5 bits; conditional E-value: 4.3
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MHCassoc_trimer 41 vdWksfEsW 49
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BA000019.orf1 29 VDWGSFTSF 37
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== domain 2 score: 0.1 bits; conditional E-value: 0.35
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HHHHHHHHHHH-TT---------HHHHHHHHHH CS
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MHCassoc_trimer 4 edqvkhLllksdPkkvfPqlketlleNLksLKk 36
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e+q k l++ + k +l++ + e L+++
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BA000019.orf1 51 EEQGKLVLQQYQ--KRIRDLQDRMGERLQKIEV 81
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556666677777..7789999999999998765 PP
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== domain 3 score: 9.5 bits; conditional E-value: 0.00038
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HHHHHH-TT---------HHHHHHHHHHH....S-HHHH CS
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MHCassoc_trimer 9 hLllksdPkkvfPqlketlleNLksLKkt....mdevdW 43
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+ +s+ ++++P+lk+ l + L++ Kk+ ++++dW
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BA000019.orf1 139 FVINESK-EQLYPDLKNPLWHHLRAVKKQqvyvVNQSDW 176
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5556666.899****************973443456666 PP
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>> DUF3498 Domain of unknown function (DUF3498)
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 9.1 1.5 0.00029 1.3 395 425 .. 43 73 .. 35 137 .. 0.81
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Alignments for each domain:
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== domain 1 score: 9.1 bits; conditional E-value: 0.00029
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------------------------------- CS
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DUF3498 395 yErRLlsQeeQaqklLleYqaRLedseeRLR 425
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y + l eeQ + +L++Yq+R+ d ++R+
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BA000019.orf1 43 YIAQVLNEEEQGKLVLQQYQKRIRDLQDRMG 73
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66788999*****************999984 PP
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Internal pipeline statistics summary:
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-------------------------------------
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Query sequence(s): 1 (198 residues)
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Target model(s): 31912 (6698792 nodes)
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Passed MSV filter: 1891 (0.0592567); expected 638.2 (0.02)
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Passed bias filter: 1237 (0.0387628); expected 638.2 (0.02)
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Passed Vit filter: 100 (0.00313362); expected 31.9 (0.001)
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Passed Fwd filter: 7 (0.000219353); expected 0.3 (1e-05)
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Initial search space (Z): 31912 [actual number of targets]
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Domain search space (domZ): 7 [number of targets reported over threshold]
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# CPU time: 0.74u 0.55s 00:00:01.29 Elapsed: 00:00:07.01
added
removed
t/data/hmmscan.out
