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# 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: mult.fasta
# target HMM database: /home/bow/db/hmmer/Pfam-A.hmm
# output directed to file: hmmer_cases/text_hmmscan_mult.out
# per-seq hits tabular output: hmmer_cases/tab_hmmscan_mult.out
# per-dom hits tabular output: hmmer_cases/domtab_hmmscan_mult.out
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: random_s00 [L=32]
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
[No hits detected that satisfy reporting thresholds]
Domain annotation for each model (and alignments):
[No targets detected that satisfy reporting thresholds]
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (32 residues)
Target model(s): 13672 (2396357 nodes)
Passed MSV filter: 338 (0.0247221); expected 273.4 (0.02)
Passed bias filter: 87 (0.00636337); expected 273.4 (0.02)
Passed Vit filter: 23 (0.00168227); expected 13.7 (0.001)
Passed Fwd filter: 14 (0.00102399); expected 0.1 (1e-05)
Initial search space (Z): 13672 [actual number of targets]
Domain search space (domZ): 0 [number of targets reported over threshold]
# CPU time: 0.20u 0.12s 00:00:00.32 Elapsed: 00:00:00.19
# Mc/sec: 403.60
//
Query: gi|4885477|ref|NP_005359.1| [L=154]
Description: myoglobin [Homo sapiens]
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-21 74.6 0.3 9.2e-21 74.0 0.2 1.3 1 Globin Globin
Domain annotation for each model (and alignments):
>> Globin Globin
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 74.0 0.2 6.7e-25 9.2e-21 1 107 [. 7 112 .. 7 113 .. 0.97
Alignments for each domain:
== domain 1 score: 74.0 bits; conditional E-value: 6.7e-25
HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHH CS
Globin 1 qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlka 81
+++lv w+kv+a+++ +g+e+l rlfk +p+t ++F kf+ l+ +++k s+++k+h+++vl al+ ++k+ ++ ++a
gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85
5789*********************************************************************...6899** PP
HHHHHHHHHHTT-.--HHHHCCHHHHH CS
Globin 82 alkklgarHakrg.vdpanfklfgeal 107
++k l+++Ha+++ ++ ++ + ++e++
gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHkIPVKYLEFISECI 112
*********************999998 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (154 residues)
Target model(s): 13672 (2396357 nodes)
Passed MSV filter: 458 (0.0334991); expected 273.4 (0.02)
Passed bias filter: 404 (0.0295494); expected 273.4 (0.02)
Passed Vit filter: 31 (0.00226741); expected 13.7 (0.001)
Passed Fwd filter: 1 (7.31422e-05); expected 0.1 (1e-05)
Initial search space (Z): 13672 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.33u 0.16s 00:00:00.49 Elapsed: 00:00:00.21
# Mc/sec: 1757.33
//
Query: gi|126362951:116-221 [L=106]
Description: leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 2 precursor [Homo sapiens]
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.4e-09 38.2 0.4 2.1e-09 37.6 0.3 1.3 1 Ig_3 Immunoglobulin domain
3.5e-05 23.7 0.1 4.3e-05 23.4 0.1 1.1 1 Ig_2 Immunoglobulin domain
Domain annotation for each model (and alignments):
>> Ig_3 Immunoglobulin domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 37.6 0.3 3e-13 2.1e-09 1 73 [. 9 84 .. 9 88 .. 0.94
Alignments for each domain:
== domain 1 score: 37.6 bits; conditional E-value: 3e-13
Ig_3 1 kPvisvspsptvtsggnvtLtCsaeggpppptisWy.....ietppelqgsegssssestLtissvtsedsgtYtCva 73
kP++s++psp+v+sggnv L+C ++ + +s + +++ +++++ ++ss +++++ +v+++ + Y+C+a
gi|126362951:116-221 9 KPTLSAQPSPVVNSGGNVILQCDSQVA--FDGFSLCkegedEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYA 84
8************************99..78888888****************************************9 PP
>> Ig_2 Immunoglobulin domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 23.4 0.1 6.2e-09 4.3e-05 1 80 [] 9 104 .. 9 104 .. 0.71
Alignments for each domain:
== domain 1 score: 23.4 bits; conditional E-value: 6.2e-09
Ig_2 1 kpvlvapp.svvtegenvtLtCsapgnptprvqwykdg.vels......qsqnq........lfipnvsaedsgtYtCra....rnseg 69
kp+l+a+p +vv++g nv L+C ++ + +++ k+g +e + + + + vs++ Y+C+a + +e+
gi|126362951:116-221 9 KPTLSAQPsPVVNSGGNVILQCDSQVA-FDGFSLCKEGeDEHPqclnsqP---HargssraiFSVGPVSPSRRWWYRCYAydsnSPYEW 93
799998885779*************85.899***9988655554443320...134455543444669************884433445 PP
Ig_2 70 gktstsveltv 80
+ +s+ +el v
gi|126362951:116-221 94 SLPSDLLELLV 104
88888888766 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (106 residues)
Target model(s): 13672 (2396357 nodes)
Passed MSV filter: 153 (0.0111908); expected 273.4 (0.02)
Passed bias filter: 143 (0.0104593); expected 273.4 (0.02)
Passed Vit filter: 11 (0.000804564); expected 13.7 (0.001)
Passed Fwd filter: 2 (0.000146284); expected 0.1 (1e-05)
Initial search space (Z): 13672 [actual number of targets]
Domain search space (domZ): 2 [number of targets reported over threshold]
# CPU time: 0.26u 0.14s 00:00:00.40 Elapsed: 00:00:00.20
# Mc/sec: 1270.07
//
Query: gi|22748937|ref|NP_065801.1| [L=1204]
Description: exportin-5 [Homo sapiens]
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
7.8e-34 116.6 7.8 1.1e-33 116.1 3.4 2.8 2 Xpo1 Exportin 1-like protein
0.0039 16.9 0.0 0.033 14.0 0.0 2.7 2 IBN_N Importin-beta N-terminal domain
Domain annotation for each model (and alignments):
>> Xpo1 Exportin 1-like protein
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 116.1 3.4 1.6e-37 1.1e-33 2 148 .] 110 271 .. 109 271 .. 0.98
2 ? -1.8 0.0 0.35 2.4e+03 112 139 .. 499 525 .. 496 529 .. 0.86
Alignments for each domain:
== domain 1 score: 116.1 bits; conditional E-value: 1.6e-37
HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHHG-HHHHHHHHHHHHHHHHHHCCS-TTTS-CCCHHHHHHHCHHHHHH CS
Xpo1 2 kflrnklaealaelflqeypnqWpsffddllsllssspsglelllriLkvlpeEiadfsrskleqerrnelkdllrsqvqk 82
+++++ l+++++e++++e+p++Wp+++ +l l++++++++el++ iL++l+e++++f ++l +rr++++++l++++++
gi|22748937|ref|NP_065801.1| 110 NHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTF--QTLPPQRRRDIQQTLTQNMER 188
89******************************************************99..79******************* PP
HHHHHHHHHC-TT-..................HHHHHHHHHHHHHHCTTS-CHHCHCS...HHHHHCHHCCSCCCHHHHHH CS
Xpo1 83 ilelllqileqsvskk...............sselveatLkclsswvswidiglivnsp..llsllfqlLndpelreaAve 146
i+++ll+ l+++v+k+ ++++ a+L++l+ +++w+++++i +++ ll++l+ lLn++el+ A+e
gi|22748937|ref|NP_065801.1| 189 IFSFLLNTLQENVNKYqqvktdtsqeskaqaNCRVGVAALNTLAGYIDWVSMSHITAENckLLEILCLLLNEQELQLGAAE 269
**************99*****************************************8889******************** PP
HH CS
Xpo1 147 cL 148
cL
gi|22748937|ref|NP_065801.1| 270 CL 271
*8 PP
== domain 2 score: -1.8 bits; conditional E-value: 0.35
HHCTTS-CHHCHCS.HHHHHCHHCCSCC CS
Xpo1 112 swvswidiglivnspllsllfqlLndpe 139
s+v+w ++l+++s +++ +f+ Ln++e
gi|22748937|ref|NP_065801.1| 499 SFVQWEAMTLFLES-VITQMFRTLNREE 525
899*********98.8888899998776 PP
>> IBN_N Importin-beta N-terminal domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 14.0 0.0 4.8e-06 0.033 4 75 .. 36 98 .. 33 100 .. 0.87
2 ? -3.3 0.0 1.2 8e+03 57 75 .. 168 186 .. 165 187 .. 0.85
Alignments for each domain:
== domain 1 score: 14.0 bits; conditional E-value: 4.8e-06
HHHHHHHSCTHHHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHSCCHHHHHHHHCS-HHHHHHHHHHHHHHH CS
IBN_N 4 qLnqlekqkPgflsallqilanksldlevRqlAalyLknlItkhWkseeaqrqqqlpeeekelIrnnllnll 75
++++++ P ++++ l+++ +k+ vR++++++L++ ++ +W+ ++ ek +++n++ +l+
gi|22748937|ref|NP_065801.1| 36 FCEEFKEKCPICVPCGLRLA-EKTQVAIVRHFGLQILEHVVKFRWN--------GMSRLEKVYLKNSVMELI 98
56788886699*********.6555899******************........999999****99999887 PP
== domain 2 score: -3.3 bits; conditional E-value: 1.2
HCS-HHHHHHHHHHHHHHH CS
IBN_N 57 qqlpeeekelIrnnllnll 75
q+lp++ + +I ++l + +
gi|22748937|ref|NP_065801.1| 168 QTLPPQRRRDIQQTLTQNM 186
6899*******99998865 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (1204 residues)
Target model(s): 13672 (2396357 nodes)
Passed MSV filter: 520 (0.0380339); expected 273.4 (0.02)
Passed bias filter: 319 (0.0233324); expected 273.4 (0.02)
Passed Vit filter: 23 (0.00168227); expected 13.7 (0.001)
Passed Fwd filter: 2 (0.000146284); expected 0.1 (1e-05)
Initial search space (Z): 13672 [actual number of targets]
Domain search space (domZ): 2 [number of targets reported over threshold]
# CPU time: 1.11u 0.17s 00:00:01.28 Elapsed: 00:00:00.72
# Mc/sec: 4007.24
//
Query: gi|125490392|ref|NP_038661.2| [L=352]
Description: POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
7e-37 124.8 0.5 1.4e-36 123.9 0.3 1.5 1 Pou Pou domain - N-terminal to homeobox domain
2.1e-18 65.5 1.1 4.1e-18 64.6 0.7 1.5 1 Homeobox Homeobox domain
------ inclusion threshold ------
0.012 15.6 0.0 0.16 12.0 0.0 2.2 2 HTH_31 Helix-turn-helix domain
0.039 13.5 0.0 0.095 12.3 0.0 1.6 1 Homeobox_KN Homeobox KN domain
0.14 10.5 0.1 0.26 9.6 0.1 1.4 1 DUF521 Protein of unknown function (DUF521)
Domain annotation for each model (and alignments):
>> Pou Pou domain - N-terminal to homeobox domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 123.9 0.3 5e-40 1.4e-36 3 75 .] 133 205 .. 131 205 .. 0.97
Alignments for each domain:
== domain 1 score: 123.9 bits; conditional E-value: 5e-40
Pou 3 eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae 75
++ ++ele+fak +kq+ri+Lg+tqadvg +lg+l+Gk+fsqttIcrFEalqLslknmckL+pllekW+eea+
gi|125490392|ref|NP_038661.2| 133 KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD 205
67899******************************************************************96 PP
>> Homeobox Homeobox domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 64.6 0.7 1.5e-21 4.1e-18 1 57 [] 224 280 .. 224 280 .. 0.98
Alignments for each domain:
== domain 1 score: 64.6 bits; conditional E-value: 1.5e-21
SS--SS--HHHHHHHHHHCCTSSS--HHHHHHHHHH----HHHHHHHHHHHHHHHHH CS
Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57
+rkRt++++ Le +F k+++ps ++++++A++lgL++++V+vWF+NrR+k k+
gi|125490392|ref|NP_038661.2| 224 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 280
79****************************************************997 PP
>> HTH_31 Helix-turn-helix domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.0 0.0 5.7e-05 0.16 1 35 [. 141 181 .. 141 184 .. 0.96
2 ? 0.8 0.0 0.19 5.2e+02 39 62 .. 245 268 .. 243 270 .. 0.86
Alignments for each domain:
== domain 1 score: 12.0 bits; conditional E-value: 5.7e-05
HTH_31 1 aLGarLralReraGLtqeevAerlg......vSastlsrlE 35
+++ +L++ R + G tq++v+ lg +S++t++r E
gi|125490392|ref|NP_038661.2| 141 QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE 181
6999***********************************99 PP
== domain 2 score: 0.8 bits; conditional E-value: 0.19
HTH_31 39 rgrpsaavlaalaralgldpaera 62
++ ps+++++ +a+ lgl+ + ++
gi|125490392|ref|NP_038661.2| 245 CPKPSLQQITHIANQLGLEKDVVR 268
678**************9988765 PP
>> Homeobox_KN Homeobox KN domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.3 0.0 3.5e-05 0.095 7 39 .. 244 276 .. 241 277 .. 0.91
Alignments for each domain:
== domain 1 score: 12.3 bits; conditional E-value: 3.5e-05
Homeobox_KN 7 hnPYPskevkeelakqTglsrkqidnWFiNaRr 39
+ P Ps +++ +a+q gl + + WF N R
gi|125490392|ref|NP_038661.2| 244 KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 276
56779*************************996 PP
>> DUF521 Protein of unknown function (DUF521)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 9.6 0.1 9.4e-05 0.26 273 334 .. 221 280 .. 197 294 .. 0.77
Alignments for each domain:
== domain 1 score: 9.6 bits; conditional E-value: 9.4e-05
DUF521 273 adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk 334
+ +++ + +++++ +++ ++l cP sl++++++a++l +k v+++ + r+ ++
gi|125490392|ref|NP_038661.2| 221 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR 280
345666667778888899************************99..9999999988876554 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (352 residues)
Target model(s): 13672 (2396357 nodes)
Passed MSV filter: 603 (0.0441047); expected 273.4 (0.02)
Passed bias filter: 465 (0.0340111); expected 273.4 (0.02)
Passed Vit filter: 44 (0.00321826); expected 13.7 (0.001)
Passed Fwd filter: 5 (0.000365711); expected 0.1 (1e-05)
Initial search space (Z): 13672 [actual number of targets]
Domain search space (domZ): 5 [number of targets reported over threshold]
# CPU time: 0.51u 0.15s 00:00:00.66 Elapsed: 00:00:00.23
# Mc/sec: 3667.47
//
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