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# hmmscan :: search sequence(s) against a profile database
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: prot_multi.fa
# target HMM database: /home/bow/db/hmmer/protdb/Pfam-A.hmm
# output directed to file: hmmscan/text_31b1_hmmscan_001.out
# per-seq hits tabular output: hmmscan/tab_31b1_hmmscan_001.out
# per-dom hits tabular output: hmmscan/domtab_31b1_hmmscan_001.out
# pfam-style tabular hit output: hmmscan/pfamtab_31b1_hmmscan_001.out
# number of worker threads: 2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: random_s00 [L=22]
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 (22 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 57 (0.0038433); expected 296.6 (0.02)
Passed bias filter: 44 (0.00296676); expected 296.6 (0.02)
Passed Vit filter: 1 (6.74263e-05); expected 14.8 (0.001)
Passed Fwd filter: 0 (0); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 0 [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:03.04
# Mc/sec: 18.89
//
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1e-22 80.5 0.3 1.6e-22 79.8 0.3 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 ! 79.8 0.3 1.1e-26 1.6e-22 1 109 [. 7 112 .. 7 113 .. 0.97
Alignments for each domain:
== domain 1 score: 79.8 bits; conditional E-value: 1.1e-26
HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHSGGGGGGSTTTTTTT-HHHHCTSHHHHHHHHHHHHHHHHHHHTTTSHHHHHH CS
Globin 1 dkalvkaswekvkanaeelgaeilkrlFkaypdtkklFkkfgdlssaedlksspkfkahakkvlaalgeavknldndealka 82
+++lv w+kv+a+++ +g+e+l rlFk +p+t ++F kf++l+s +++k s+++k+h+++vl+alg ++k+ ++ ++a
gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85
5789*********************************************************************...689*** PP
HHHHHHHHHHTSTT--HHHHHHHHHHH CS
Globin 83 alkklaarHaergkvdpanFklfgeal 109
+k la++Ha+++k++ ++ + ++e++
gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHKIPVKYLEFISECI 112
************************998 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (154 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 494 (0.0333086); expected 296.6 (0.02)
Passed bias filter: 402 (0.0271054); expected 296.6 (0.02)
Passed Vit filter: 35 (0.00235992); expected 14.8 (0.001)
Passed Fwd filter: 1 (6.74263e-05); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:03.72
# Mc/sec: 108.06
//
Query: gi|126362951|ref|NP_001075106.1| [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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
9.3e-10 38.8 0.4 1.4e-09 38.3 0.4 1.3 1 Ig_3 Immunoglobulin domain
1.6e-06 28.1 0.1 2e-06 27.8 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 ! 38.3 0.4 1.8e-13 1.4e-09 1 73 [. 8 83 .. 8 87 .. 0.95
Alignments for each domain:
== domain 1 score: 38.3 bits; conditional E-value: 1.8e-13
Ig_3 1 kPvisvspsptvtsggnvtLtCsaeggpppptisWy.....ietppelqgsegssssestLtissvtsedsGtYtCva 73
kP++s++psp+v+sggnv L+C ++ + +s + +++ +++++ ++ss +++++ +v+++ + Y+C+a
gi|126362951|ref|NP_001075106.1| 8 KPTLSAQPSPVVNSGGNVILQCDSQVA--FDGFSLCkegedEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYA 83
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 ! 27.8 0.1 2.6e-10 2e-06 1 80 [] 8 103 .. 8 103 .. 0.75
Alignments for each domain:
== domain 1 score: 27.8 bits; conditional E-value: 2.6e-10
Ig_2 1 kpvlsapp.tvvtegenvtLtCqapgnptpkvqwykdg.....eelsqsqna.......lfipnvsaedsGtYtCra 64
kp+lsa+p +vv+ g nv L C ++ ++ +++ k+g + l++++ a + + vs++ Y+C+a
gi|126362951|ref|NP_001075106.1| 8 KPTLSAQPsPVVNSGGNVILQCDSQVA-FDGFSLCKEGedehpQCLNSQPHArgssraiFSVGPVSPSRRWWYRCYA 83
799**9997779*************86.9*******98643333333333335555553444669************ PP
Ig_2 65 ....snsegskqsnsvevtv 80
s +e+s +s+ +e+ v
gi|126362951|ref|NP_001075106.1| 84 ydsnSPYEWSLPSDLLELLV 103
88554455699999999876 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (106 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 171 (0.0115299); expected 296.6 (0.02)
Passed bias filter: 140 (0.00943969); expected 296.6 (0.02)
Passed Vit filter: 11 (0.00074169); expected 14.8 (0.001)
Passed Fwd filter: 2 (0.000134853); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 2 [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:01.22
# Mc/sec: 226.80
//
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
8.5e-34 116.6 7.8 1.2e-33 116.1 4.9 2.8 2 Xpo1 Exportin 1-like protein
0.0044 16.9 0.0 0.036 13.9 0.0 2.7 2 IBN_N Importin-beta N-terminal domain
------ inclusion threshold ------
0.095 11.7 0.3 1.3 8.0 0.3 2.3 2 Rac1 Rac1-binding 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 4.9 2.3e-37 1.2e-33 2 148 .] 110 271 .. 109 271 .. 0.98
2 ? -1.8 0.0 0.52 2.6e+03 112 139 .. 499 525 .. 496 529 .. 0.86
Alignments for each domain:
== domain 1 score: 116.1 bits; conditional E-value: 2.3e-37
HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHCTSXTTCSHHHHHHHHHHHHHHHHHH 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
HHHHHHHHHHHHHHCC...............HHHHHHHHHHHHHHHTTTS-HHHHHSSC..HHHHHHHHTTSCCCHHHHHH 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: 0.52
HHTTTS-HHHHHSSCHHHHHHHHTTSCC 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 ! 13.9 0.0 7.3e-06 0.036 4 75 .. 36 98 .. 33 100 .. 0.87
2 ? -3.5 0.0 2 1e+04 57 74 .. 168 185 .. 165 186 .. 0.84
Alignments for each domain:
== domain 1 score: 13.9 bits; conditional E-value: 7.3e-06
HHHHHHHSTTHHHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHSCCHHHHHHHHCSSHHHHHHHHHHHHHHH 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: -3.5 bits; conditional E-value: 2
HCSSHHHHHHHHHHHHHH CS
IBN_N 57 qqlpeeekelIrnnllnl 74
q+lp++ + +I ++l +
gi|22748937|ref|NP_065801.1| 168 QTLPPQRRRDIQQTLTQN 185
6899*******9999876 PP
>> Rac1 Rac1-binding domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 8.0 0.3 0.00026 1.3 94 171 .. 89 169 .. 82 254 .. 0.75
2 ? 0.8 0.0 0.041 2e+02 150 181 .. 310 341 .. 296 354 .. 0.82
Alignments for each domain:
== domain 1 score: 8.0 bits; conditional E-value: 0.00026
Rac1 94 qlrsnimksvvepslkriqkqldqshslvdia..slerar.khletllevlvtlsqqgekvssevydflyrlaevkvslsv 171
+l++ +m +++ +l+ ++++ +l+ i ++r +h +l l tls+qge + v +l rlae v++
gi|22748937|ref|NP_065801.1| 89 YLKNSVMELIANGTLNILEEENHIKDALSRIVveMIKREWpQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTFQT 169
788899999******9998766666666666511555543499*9*****************999999******9888642 PP
== domain 2 score: 0.8 bits; conditional E-value: 0.041
Rac1 150 kvssevydflyrlaevkvslsvrldtlkqqqe 181
+ + y fl+rl +v +l+ +l +l + +
gi|22748937|ref|NP_065801.1| 310 GLVEKHYVFLKRLCQVLCALGNQLCALLGADS 341
556678******************99977665 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (1204 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 567 (0.0382307); expected 296.6 (0.02)
Passed bias filter: 414 (0.0279145); expected 296.6 (0.02)
Passed Vit filter: 32 (0.00215764); expected 14.8 (0.001)
Passed Fwd filter: 3 (0.000202279); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 3 [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:03.60
# Mc/sec: 873.01
//
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
7.6e-37 124.8 0.5 1.5e-36 123.9 0.5 1.5 1 Pou Pou domain - N-terminal to homeobox domain
1.8e-18 65.8 1.1 3.4e-18 64.9 1.1 1.5 1 Homeobox Homeobox domain
------ inclusion threshold ------
0.013 15.6 0.0 0.18 12.0 0.0 2.2 2 HTH_31 Helix-turn-helix domain
0.043 13.5 0.0 0.1 12.2 0.0 1.6 1 Homeobox_KN Homeobox KN domain
0.15 10.5 0.1 0.28 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 0.5 5e-40 1.5e-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 ! 64.9 1.1 1.2e-21 3.4e-18 1 57 [] 224 280 .. 224 280 .. 0.98
Alignments for each domain:
== domain 1 score: 64.9 bits; conditional E-value: 1.2e-21
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC 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 5.9e-05 0.18 1 35 [. 141 181 .. 141 185 .. 0.95
2 ? 0.9 0.0 0.18 5.3e+02 39 62 .. 245 268 .. 243 270 .. 0.85
Alignments for each domain:
== domain 1 score: 12.0 bits; conditional E-value: 5.9e-05
HTH_31 1 aLGarLralReraGLsqeevAerag......vSastlsriE 35
+++ +L++ R + G +q++v+ +g +S++t++r E
gi|125490392|ref|NP_038661.2| 141 QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE 181
7999**************************99*******99 PP
== domain 2 score: 0.9 bits; conditional E-value: 0.18
HTH_31 39 rgrpslavlaalaralgldeaera 62
++ psl++++ +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 ? 12.2 0.0 3.5e-05 0.1 7 39 .. 244 276 .. 241 277 .. 0.91
Alignments for each domain:
== domain 1 score: 12.2 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 0.28 273 334 .. 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 searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 663 (0.0447037); expected 296.6 (0.02)
Passed bias filter: 493 (0.0332412); expected 296.6 (0.02)
Passed Vit filter: 45 (0.00303419); expected 14.8 (0.001)
Passed Fwd filter: 5 (0.000337132); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 5 [number of targets reported over threshold]
# CPU time: 0.43u 0.33s 00:00:00.76 Elapsed: 00:00:04.08
# Mc/sec: 225.21
//
[ok]
|
