# hmmscan :: search sequence(s) against a profile database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: BA000019.orf1.fasta
# target HMM database: /data/biodata/HMMerDB/Pfam.hmm
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: BA000019.orf1 [L=198]
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
6e-30 105.2 0.3 6.7e-30 105.0 0.2 1.0 1 Peripla_BP_2 Periplasmic binding protein
------ inclusion threshold ------
0.036 14.7 0.0 0.09 13.4 0.0 1.7 1 DUF2726 Protein of unknown function (DUF2726)
0.039 14.1 0.3 0.049 13.8 0.2 1.1 1 Pfam-B_1590
0.22 12.5 0.0 0.33 12.0 0.0 1.3 1 Pfam-B_6580
0.25 12.1 0.2 0.37 11.5 0.2 1.2 1 Calpain_III Calpain large subunit, domain III
0.42 11.5 1.2 1.7 9.5 0.1 2.3 3 MHCassoc_trimer Class II MHC-associated invariant chain trim
1.2 9.2 2.2 1.3 9.1 1.5 1.1 1 DUF3498 Domain of unknown function (DUF3498)
Domain annotation for each model (and alignments):
>> Peripla_BP_2 Periplasmic binding protein
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 105.0 0.2 1.5e-33 6.7e-30 59 236 .. 2 173 .. 1 175 [. 0.93
Alignments for each domain:
== domain 1 score: 105.0 bits; conditional E-value: 1.5e-33
Peripla_BP_2 59 lkPDlvivsafgalvseieellelgipvvavessstaeslleqirllgellgeedeaeelvaelesridavkaridsl.kpktvlvfgyadegikv 153
lkPDl+i+ +++ ++i+++l++ +p+v v+ s+ s+++ +r ++++l+ee++++ + +++++ri+++++r + ++ +v+v+g+++ +ik+
BA000019.orf1 2 LKPDLIIGREYQ---KNIYNQLSNFAPTVLVDWGSF-TSFQDNFRYIAQVLNEEEQGKLVLQQYQKRIRDLQDRMGERlQKIEVSVIGFSGQSIKS 93
8***********...********************9.*****************************************999999999999997777 PP
Peripla_BP_2 154 vfgsgswvgdlldaaggeni.iaeakgseseeisaEqilaadpdviivsgrgedtktgveelkenplwaelpAvkngrvyllds 236
++ + ++++ld+ag++ i i++++++ + eis+E+++++d+dv++v k+ + ++nplw +l+Avk+++vy++++
BA000019.orf1 94 LNR-DAVFNQVLDDAGIKRIsIQKNQQERYLEISIENLNKYDADVLFVINE---SKEQLYPDLKNPLWHHLRAVKKQQVYVVNQ 173
776.5678999999****99777777*************************...77777777899***************9976 PP
>> DUF2726 Protein of unknown function (DUF2726)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.4 0.0 2e-05 0.09 79 112 .. 86 119 .. 79 130 .. 0.75
Alignments for each domain:
== domain 1 score: 13.4 bits; conditional E-value: 2e-05
DUF2726 79 ashkqgkaekrDalkeealekAgipllrvkakks 112
+s ++ k +rDa+++++l+ Agi+ + +++ ++
BA000019.orf1 86 FSGQSIKSLNRDAVFNQVLDDAGIKRISIQKNQQ 119
4555777999****************99954433 PP
>> Pfam-B_1590
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.8 0.2 1.1e-05 0.049 6 102 .. 78 169 .. 74 195 .. 0.75
Alignments for each domain:
== domain 1 score: 13.8 bits; conditional E-value: 1.1e-05
Pfam-B_1590 6 risafinlfiGqsvsrktivnail.slleqkGflkrswnkinlpctyvnlsieriskfdflpilskikgkeisyklyGeteWqtidklLlnvnkhk 100
+i + f Gqs++ + +a++ +l++ G + s +k n y+++sie+++k+d ++ + ke +y + + W+++ v+k++
BA000019.orf1 78 KIEVSVIGFSGQSIKSLNR-DAVFnQVLDDAGIKRISIQK-NQQERYLEISIENLNKYDADVLFVINESKEQLYPDLKNPLWHHLR----AVKKQQ 167
5666666789999876554.34441578999999999988.56789*************98888888899****999999997654....444444 PP
Pfam-B_1590 101 af 102
++
BA000019.orf1 168 VY 169
44 PP
>> Pfam-B_6580
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.0 0.0 7.2e-05 0.33 36 89 .. 70 124 .. 61 139 .. 0.83
Alignments for each domain:
== domain 1 score: 12.0 bits; conditional E-value: 7.2e-05
Pfam-B_6580 36 ewLedrlataaaAalvldalqseelpr.alqrelLeaigakavvlrkdqtrrlla 89
+++ +rl+++++ + + + l+r a+ +++L+ +g+k + ++k+q+ r l
BA000019.orf1 70 DRMGERLQKIEVSVIGFSGQSIKSLNRdAVFNQVLDDAGIKRISIQKNQQERYLE 124
5677889999999999999988888862699******************999764 PP
>> Calpain_III Calpain large subunit, domain III
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.5 0.2 8.1e-05 0.37 25 91 .. 35 102 .. 31 129 .. 0.75
Alignments for each domain:
== domain 1 score: 11.5 bits; conditional E-value: 8.1e-05
Calpain_III 25 etfltNPqfrlslkepddedctvliaLmqknrrkkrkk.geenltigfavykv.kkkekeldkeffkkn 91
+f +N + ++ +++++ +++++ +qk+ r ++ ge++ i+++v+ +++ k+l+++++ ++
BA000019.orf1 35 TSFQDNFRYIAQVLNEEEQ-GKLVLQQYQKRIRDLQDRmGERLQKIEVSVIGFsGQSIKSLNRDAVFNQ 102
48999**********9987.7999999999988776655888888999998887777788888766555 PP
>> MHCassoc_trimer Class II MHC-associated invariant chain trimerisation domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -3.5 0.0 4.3 2e+04 41 49 .. 29 37 .. 27 41 .. 0.78
2 ? 0.1 0.0 0.35 1.6e+03 4 36 .. 51 81 .. 49 96 .. 0.74
3 ? 9.5 0.1 0.00038 1.7 9 43 .. 139 176 .. 131 178 .. 0.73
Alignments for each domain:
== domain 1 score: -3.5 bits; conditional E-value: 4.3
HHHHHHHHH CS
MHCassoc_trimer 41 vdWksfEsW 49
vdW sf s+
BA000019.orf1 29 VDWGSFTSF 37
689999886 PP
== domain 2 score: 0.1 bits; conditional E-value: 0.35
HHHHHHHHHHH-TT---------HHHHHHHHHH CS
MHCassoc_trimer 4 edqvkhLllksdPkkvfPqlketlleNLksLKk 36
e+q k l++ + k +l++ + e L+++
BA000019.orf1 51 EEQGKLVLQQYQ--KRIRDLQDRMGERLQKIEV 81
556666677777..7789999999999998765 PP
== domain 3 score: 9.5 bits; conditional E-value: 0.00038
HHHHHH-TT---------HHHHHHHHHHH....S-HHHH CS
MHCassoc_trimer 9 hLllksdPkkvfPqlketlleNLksLKkt....mdevdW 43
+ +s+ ++++P+lk+ l + L++ Kk+ ++++dW
BA000019.orf1 139 FVINESK-EQLYPDLKNPLWHHLRAVKKQqvyvVNQSDW 176
5556666.899****************973443456666 PP
>> DUF3498 Domain of unknown function (DUF3498)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 9.1 1.5 0.00029 1.3 395 425 .. 43 73 .. 35 137 .. 0.81
Alignments for each domain:
== domain 1 score: 9.1 bits; conditional E-value: 0.00029
------------------------------- CS
DUF3498 395 yErRLlsQeeQaqklLleYqaRLedseeRLR 425
y + l eeQ + +L++Yq+R+ d ++R+
BA000019.orf1 43 YIAQVLNEEEQGKLVLQQYQKRIRDLQDRMG 73
66788999*****************999984 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (198 residues)
Target model(s): 31912 (6698792 nodes)
Passed MSV filter: 1891 (0.0592567); expected 638.2 (0.02)
Passed bias filter: 1237 (0.0387628); expected 638.2 (0.02)
Passed Vit filter: 100 (0.00313362); expected 31.9 (0.001)
Passed Fwd filter: 7 (0.000219353); expected 0.3 (1e-05)
Initial search space (Z): 31912 [actual number of targets]
Domain search space (domZ): 7 [number of targets reported over threshold]
# CPU time: 0.74u 0.55s 00:00:01.29 Elapsed: 00:00:07.01
# Mc/sec: 189.21
//