| blob | 65edacc6eb07066795173961ead9de4a90c4a00f |
1 # hmmscan :: search sequence(s) against a profile database
2 # HMMER 3.0 (March 2010); http://hmmer.org/
3 # Copyright (C) 2010 Howard Hughes Medical Institute.
4 # Freely distributed under the GNU General Public License (GPLv3).
5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
6 # query sequence file: BA000019.orf1.fasta
7 # target HMM database: /data/biodata/HMMerDB/Pfam.hmm
8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
10 Query: BA000019.orf1 [L=198]
11 Scores for complete sequence (score includes all domains):
12 --- full sequence --- --- best 1 domain --- -#dom-
13 E-value score bias E-value score bias exp N Model Description
14 ------- ------ ----- ------- ------ ----- ---- -- -------- -----------
15 6e-30 105.2 0.3 6.7e-30 105.0 0.2 1.0 1 Peripla_BP_2 Periplasmic binding protein
16 ------ inclusion threshold ------
17 0.036 14.7 0.0 0.09 13.4 0.0 1.7 1 DUF2726 Protein of unknown function (DUF2726)
18 0.039 14.1 0.3 0.049 13.8 0.2 1.1 1 Pfam-B_1590
19 0.22 12.5 0.0 0.33 12.0 0.0 1.3 1 Pfam-B_6580
20 0.25 12.1 0.2 0.37 11.5 0.2 1.2 1 Calpain_III Calpain large subunit, domain III
21 0.42 11.5 1.2 1.7 9.5 0.1 2.3 3 MHCassoc_trimer Class II MHC-associated invariant chain trim
22 1.2 9.2 2.2 1.3 9.1 1.5 1.1 1 DUF3498 Domain of unknown function (DUF3498)
25 Domain annotation for each model (and alignments):
26 >> Peripla_BP_2 Periplasmic binding protein
27 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
28 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
29 1 ! 105.0 0.2 1.5e-33 6.7e-30 59 236 .. 2 173 .. 1 175 [. 0.93
31 Alignments for each domain:
32 == domain 1 score: 105.0 bits; conditional E-value: 1.5e-33
33 Peripla_BP_2 59 lkPDlvivsafgalvseieellelgipvvavessstaeslleqirllgellgeedeaeelvaelesridavkaridsl.kpktvlvfgyadegikv 153
34 lkPDl+i+ +++ ++i+++l++ +p+v v+ s+ s+++ +r ++++l+ee++++ + +++++ri+++++r + ++ +v+v+g+++ +ik+
35 BA000019.orf1 2 LKPDLIIGREYQ---KNIYNQLSNFAPTVLVDWGSF-TSFQDNFRYIAQVLNEEEQGKLVLQQYQKRIRDLQDRMGERlQKIEVSVIGFSGQSIKS 93
36 8***********...********************9.*****************************************999999999999997777 PP
38 Peripla_BP_2 154 vfgsgswvgdlldaaggeni.iaeakgseseeisaEqilaadpdviivsgrgedtktgveelkenplwaelpAvkngrvyllds 236
39 ++ + ++++ld+ag++ i i++++++ + eis+E+++++d+dv++v k+ + ++nplw +l+Avk+++vy++++
40 BA000019.orf1 94 LNR-DAVFNQVLDDAGIKRIsIQKNQQERYLEISIENLNKYDADVLFVINE---SKEQLYPDLKNPLWHHLRAVKKQQVYVVNQ 173
41 776.5678999999****99777777*************************...77777777899***************9976 PP
43 >> DUF2726 Protein of unknown function (DUF2726)
44 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
45 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
46 1 ? 13.4 0.0 2e-05 0.09 79 112 .. 86 119 .. 79 130 .. 0.75
48 Alignments for each domain:
49 == domain 1 score: 13.4 bits; conditional E-value: 2e-05
50 DUF2726 79 ashkqgkaekrDalkeealekAgipllrvkakks 112
51 +s ++ k +rDa+++++l+ Agi+ + +++ ++
52 BA000019.orf1 86 FSGQSIKSLNRDAVFNQVLDDAGIKRISIQKNQQ 119
53 4555777999****************99954433 PP
55 >> Pfam-B_1590
56 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
57 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
58 1 ? 13.8 0.2 1.1e-05 0.049 6 102 .. 78 169 .. 74 195 .. 0.75
60 Alignments for each domain:
61 == domain 1 score: 13.8 bits; conditional E-value: 1.1e-05
62 Pfam-B_1590 6 risafinlfiGqsvsrktivnail.slleqkGflkrswnkinlpctyvnlsieriskfdflpilskikgkeisyklyGeteWqtidklLlnvnkhk 100
63 +i + f Gqs++ + +a++ +l++ G + s +k n y+++sie+++k+d ++ + ke +y + + W+++ v+k++
64 BA000019.orf1 78 KIEVSVIGFSGQSIKSLNR-DAVFnQVLDDAGIKRISIQK-NQQERYLEISIENLNKYDADVLFVINESKEQLYPDLKNPLWHHLR----AVKKQQ 167
65 5666666789999876554.34441578999999999988.56789*************98888888899****999999997654....444444 PP
67 Pfam-B_1590 101 af 102
68 ++
69 BA000019.orf1 168 VY 169
70 44 PP
72 >> Pfam-B_6580
73 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
74 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
75 1 ? 12.0 0.0 7.2e-05 0.33 36 89 .. 70 124 .. 61 139 .. 0.83
77 Alignments for each domain:
78 == domain 1 score: 12.0 bits; conditional E-value: 7.2e-05
79 Pfam-B_6580 36 ewLedrlataaaAalvldalqseelpr.alqrelLeaigakavvlrkdqtrrlla 89
80 +++ +rl+++++ + + + l+r a+ +++L+ +g+k + ++k+q+ r l
81 BA000019.orf1 70 DRMGERLQKIEVSVIGFSGQSIKSLNRdAVFNQVLDDAGIKRISIQKNQQERYLE 124
82 5677889999999999999988888862699******************999764 PP
84 >> Calpain_III Calpain large subunit, domain III
85 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
86 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
87 1 ? 11.5 0.2 8.1e-05 0.37 25 91 .. 35 102 .. 31 129 .. 0.75
89 Alignments for each domain:
90 == domain 1 score: 11.5 bits; conditional E-value: 8.1e-05
91 Calpain_III 25 etfltNPqfrlslkepddedctvliaLmqknrrkkrkk.geenltigfavykv.kkkekeldkeffkkn 91
92 +f +N + ++ +++++ +++++ +qk+ r ++ ge++ i+++v+ +++ k+l+++++ ++
93 BA000019.orf1 35 TSFQDNFRYIAQVLNEEEQ-GKLVLQQYQKRIRDLQDRmGERLQKIEVSVIGFsGQSIKSLNRDAVFNQ 102
94 48999**********9987.7999999999988776655888888999998887777788888766555 PP
96 >> MHCassoc_trimer Class II MHC-associated invariant chain trimerisation domain
97 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
98 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
99 1 ? -3.5 0.0 4.3 2e+04 41 49 .. 29 37 .. 27 41 .. 0.78
100 2 ? 0.1 0.0 0.35 1.6e+03 4 36 .. 51 81 .. 49 96 .. 0.74
101 3 ? 9.5 0.1 0.00038 1.7 9 43 .. 139 176 .. 131 178 .. 0.73
103 Alignments for each domain:
104 == domain 1 score: -3.5 bits; conditional E-value: 4.3
105 HHHHHHHHH CS
106 MHCassoc_trimer 41 vdWksfEsW 49
107 vdW sf s+
108 BA000019.orf1 29 VDWGSFTSF 37
109 689999886 PP
111 == domain 2 score: 0.1 bits; conditional E-value: 0.35
112 HHHHHHHHHHH-TT---------HHHHHHHHHH CS
113 MHCassoc_trimer 4 edqvkhLllksdPkkvfPqlketlleNLksLKk 36
114 e+q k l++ + k +l++ + e L+++
115 BA000019.orf1 51 EEQGKLVLQQYQ--KRIRDLQDRMGERLQKIEV 81
116 556666677777..7789999999999998765 PP
118 == domain 3 score: 9.5 bits; conditional E-value: 0.00038
119 HHHHHH-TT---------HHHHHHHHHHH....S-HHHH CS
120 MHCassoc_trimer 9 hLllksdPkkvfPqlketlleNLksLKkt....mdevdW 43
121 + +s+ ++++P+lk+ l + L++ Kk+ ++++dW
122 BA000019.orf1 139 FVINESK-EQLYPDLKNPLWHHLRAVKKQqvyvVNQSDW 176
123 5556666.899****************973443456666 PP
125 >> DUF3498 Domain of unknown function (DUF3498)
126 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
127 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
128 1 ? 9.1 1.5 0.00029 1.3 395 425 .. 43 73 .. 35 137 .. 0.81
130 Alignments for each domain:
131 == domain 1 score: 9.1 bits; conditional E-value: 0.00029
132 ------------------------------- CS
133 DUF3498 395 yErRLlsQeeQaqklLleYqaRLedseeRLR 425
134 y + l eeQ + +L++Yq+R+ d ++R+
135 BA000019.orf1 43 YIAQVLNEEEQGKLVLQQYQKRIRDLQDRMG 73
136 66788999*****************999984 PP
140 Internal pipeline statistics summary:
141 -------------------------------------
142 Query sequence(s): 1 (198 residues)
143 Target model(s): 31912 (6698792 nodes)
144 Passed MSV filter: 1891 (0.0592567); expected 638.2 (0.02)
145 Passed bias filter: 1237 (0.0387628); expected 638.2 (0.02)
146 Passed Vit filter: 100 (0.00313362); expected 31.9 (0.001)
147 Passed Fwd filter: 7 (0.000219353); expected 0.3 (1e-05)
148 Initial search space (Z): 31912 [actual number of targets]
149 Domain search space (domZ): 7 [number of targets reported over threshold]
150 # CPU time: 0.74u 0.55s 00:00:01.29 Elapsed: 00:00:07.01
151 # Mc/sec: 189.21
152 //
153 Query: lcl|Test_ID.1|P1 [L=463]
154 Description: 281521..282909
155 Scores for complete sequence (score includes all domains):
156 --- full sequence --- --- best 1 domain --- -#dom-
157 E-value score bias E-value score bias exp N Model Description
158 ------- ------ ----- ------- ------ ----- ---- -- -------- -----------
159 2.2e-06 19.9 1.5 4.3e-06 18.9 1.0 1.4 1 IS4.original
160 2.3e-06 19.7 1.5 4.3e-06 18.8 1.0 1.4 1 IS4.original
163 Domain annotation for each model (and alignments):
164 >> IS4.original
165 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
166 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
167 1 ! 18.9 1.0 8.9e-08 4.3e-06 315 353 .. 335 369 .. 318 391 .. 0.75
169 Alignments for each domain:
170 == domain 1 score: 18.9 bits; conditional E-value: 8.9e-08
171 IS4.original 315 filatnlddeldaediaelYrlRwqiElfFrelKsllgl 353
172 lat+ +el+ae+i+ lY +Rw+iE +F+ lK ++
173 lcl|Test_ID.1|P1 335 LLLATE--TELSAEEILRLYARRWGIEPLFHNLKR--WW 369
174 345555..**************************7..44 PP
176 >> IS4.original
177 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
178 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
179 1 ! 18.8 1.0 9e-08 4.3e-06 315 353 .. 335 369 .. 318 391 .. 0.75
181 Alignments for each domain:
182 == domain 1 score: 18.8 bits; conditional E-value: 9e-08
183 IS4.original 315 filatnlddeldaediaelYrlRwqiElfFrelKsllgl 353
184 lat+ +el+ae+i+ lY +Rw+iE +F+ lK ++
185 lcl|Test_ID.1|P1 335 LLLATE--TELSAEEILRLYARRWGIEPLFHNLKR--WW 369
186 345555..**************************7..44 PP
190 Internal pipeline statistics summary:
191 -------------------------------------
192 Query sequence(s): 1 (463 residues)
193 Target model(s): 96 (37031 nodes)
194 Passed MSV filter: 16 (0.166667); expected 1.9 (0.02)
195 Passed bias filter: 16 (0.166667); expected 1.9 (0.02)
196 Passed Vit filter: 9 (0.09375); expected 0.1 (0.001)
197 Passed Fwd filter: 2 (0.0208333); expected 0.0 (1e-05)
198 Initial search space (Z): 96 [actual number of targets]
199 Domain search space (domZ): 2 [number of targets reported over threshold]
200 # CPU time: 0.03u 0.02s 00:00:00.04 Elapsed: 00:00:00.06
201 # Mc/sec: 276.54
202 //