# 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]