# hmmsearch :: search profile(s) against a sequence database # HMMER 3.0b3 (November 2009); http://hmmer.org/ # Copyright (C) 2009 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: domain1.hmmer # target sequence database: /home/chengji/software/prosys_database/cm_lib/pdb_cm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: domain1.fasta [M=196] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-90 303.8 0.0 4.5e-90 303.6 0.0 1.0 1 3BOJA 4.3e-90 303.7 0.0 4.8e-90 303.5 0.0 1.0 1 3BOHA 2.7e-87 294.5 0.0 3e-87 294.4 0.0 1.0 1 3UK8B 2.9e-87 294.4 0.0 3.3e-87 294.2 0.0 1.0 1 3UK8A 8.8e-87 292.8 0.0 9.9e-87 292.7 0.0 1.0 1 3BOBA Domain annotation for each sequence (and alignments): >> 3BOJA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 303.6 0.0 1.2e-94 4.5e-90 1 196 [] 6 206 .. 6 206 .. 0.99 Alignments for each domain: == domain 1 score: 303.6 bits; conditional E-value: 1.2e-94 domain1.fasta 1 ivea.qkrgWeveivkass....lvkvkpagvlkCvDgRksdgkrksgpkilGgvlaiaanrgvgttegleqitkevkakGhvpgvHgdehgeklg 91 iv+a q+rgW++eiv++ s +v+v+p+g+lkCvDgR+sd+++++gpk++Gg++aia+nrgv+t+egl+qitkev++kGhvp+vHgd+++++lg 3BOJA 6 IVAAlQERGWQAEIVTEFSllneMVDVDPQGILKCVDGRGSDNTQFCGPKMPGGIYAIAHNRGVTTLEGLKQITKEVASKGHVPSVHGDHSSDMLG 101 57788************999**************************************************************************** PP domain1.fasta 92 CGffklwltgkladvglprpefsaeelaeiveeaggvveelkGkHeekvvvlNfvpgtTlepnaedqrFvvDaWaadklgldveklleaaaatVel 187 CGffklw+tg+++d+g+prp+f+a+++a++ve+aggv+e+++G+H+ekvv++N+v+++Tlep+++dqrF+vD+Waa+k+gldv+k+l aaaatVe+ 3BOJA 102 CGFFKLWVTGRFDDMGYPRPQFDADQGAKAVENAGGVIEMHHGSHAEKVVYINLVENKTLEPDEDDQRFIVDGWAAGKFGLDVPKFLIAAAATVEM 197 ************************************************************************************************ PP domain1.fasta 188 Lsgpkiaki 196 L+gpk+aki 3BOJA 198 LGGPKKAKI 206 *******98 PP >> 3BOHA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 303.5 0.0 1.3e-94 4.8e-90 1 196 [] 10 210 .. 10 210 .. 0.99 Alignments for each domain: == domain 1 score: 303.5 bits; conditional E-value: 1.3e-94 domain1.fasta 1 ivea.qkrgWeveivkass....lvkvkpagvlkCvDgRksdgkrksgpkilGgvlaiaanrgvgttegleqitkevkakGhvpgvHgdehgeklg 91 iv+a q+rgW++eiv++ s +v+v+p+g+lkCvDgR+sd+++++gpk++Gg++aia+nrgv+t+egl+qitkev++kGhvp+vHgd+++++lg 3BOHA 10 IVAAlQERGWQAEIVTEFSllneMVDVDPQGILKCVDGRGSDNTQFCGPKMPGGIYAIAHNRGVTTLEGLKQITKEVASKGHVPSVHGDHSSDMLG 105 57788************999**************************************************************************** PP domain1.fasta 92 CGffklwltgkladvglprpefsaeelaeiveeaggvveelkGkHeekvvvlNfvpgtTlepnaedqrFvvDaWaadklgldveklleaaaatVel 187 CGffklw+tg+++d+g+prp+f+a+++a++ve+aggv+e+++G+H+ekvv++N+v+++Tlep+++dqrF+vD+Waa+k+gldv+k+l aaaatVe+ 3BOHA 106 CGFFKLWVTGRFDDMGYPRPQFDADQGAKAVENAGGVIEMHHGSHAEKVVYINLVENKTLEPDEDDQRFIVDGWAAGKFGLDVPKFLIAAAATVEM 201 ************************************************************************************************ PP domain1.fasta 188 Lsgpkiaki 196 L+gpk+aki 3BOHA 202 LGGPKKAKI 210 *******98 PP >> 3UK8B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 294.4 0.0 8.3e-92 3e-87 1 196 [] 6 206 .. 6 206 .. 0.99 Alignments for each domain: == domain 1 score: 294.4 bits; conditional E-value: 8.3e-92 domain1.fasta 1 ivea.qkrgWeveivkass....lvkvkpagvlkCvDgRksdgkrksgpkilGgvlaiaanrgvgttegleqitkevkakGhvpgvHgdehgeklg 91 iv+a ++rgW+++ivkas+ l +v+p+g+lkCvDgR+sd++++ gpk++Gg++aia+nrgv+t+egl++it+ev++kGhvp+vHgd+++++lg 3UK8B 6 IVSAlRGRGWKASIVKASTmsseLKRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAIAHNRGVTTLEGLKDITREVASKGHVPSVHGDHSSDMLG 101 567889************999*************************************************************************** PP domain1.fasta 92 CGffklwltgkladvglprpefsaeelaeiveeaggvveelkGkHeekvvvlNfvpgtTlepnaedqrFvvDaWaadklgldveklleaaaatVel 187 CGffklwltg+++d+g+prpef+a+++a +v++aggv+e+++G+Heekvv++N+v+g+Tlepn++dqrF+vD+Waa+k+gldv k+l+aaaatVe+ 3UK8B 102 CGFFKLWLTGRFDDMGYPRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNEHDQRFIVDGWAASKFGLDVVKFLVAAAATVEM 197 ************************************************************************************************ PP domain1.fasta 188 Lsgpkiaki 196 L+gpk+aki 3UK8B 198 LGGPKKAKI 206 *******98 PP >> 3UK8A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 294.2 0.0 9.1e-92 3.3e-87 1 196 [] 11 211 .. 11 211 .. 0.99 Alignments for each domain: == domain 1 score: 294.2 bits; conditional E-value: 9.1e-92 domain1.fasta 1 ivea.qkrgWeveivkass....lvkvkpagvlkCvDgRksdgkrksgpkilGgvlaiaanrgvgttegleqitkevkakGhvpgvHgdehgeklg 91 iv+a ++rgW+++ivkas+ l +v+p+g+lkCvDgR+sd++++ gpk++Gg++aia+nrgv+t+egl++it+ev++kGhvp+vHgd+++++lg 3UK8A 11 IVSAlRGRGWKASIVKASTmsseLKRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAIAHNRGVTTLEGLKDITREVASKGHVPSVHGDHSSDMLG 106 567889************999*************************************************************************** PP domain1.fasta 92 CGffklwltgkladvglprpefsaeelaeiveeaggvveelkGkHeekvvvlNfvpgtTlepnaedqrFvvDaWaadklgldveklleaaaatVel 187 CGffklwltg+++d+g+prpef+a+++a +v++aggv+e+++G+Heekvv++N+v+g+Tlepn++dqrF+vD+Waa+k+gldv k+l+aaaatVe+ 3UK8A 107 CGFFKLWLTGRFDDMGYPRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNEHDQRFIVDGWAASKFGLDVVKFLVAAAATVEM 202 ************************************************************************************************ PP domain1.fasta 188 Lsgpkiaki 196 L+gpk+aki 3UK8A 203 LGGPKKAKI 211 *******98 PP >> 3BOBA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 292.7 0.0 2.7e-91 9.9e-87 2 196 .] 7 206 .. 6 206 .. 0.99 Alignments for each domain: == domain 1 score: 292.7 bits; conditional E-value: 2.7e-91 domain1.fasta 2 vea.qkrgWeveivkass....lvkvkpagvlkCvDgRksdgkrksgpkilGgvlaiaanrgvgttegleqitkevkakGhvpgvHgdehgeklgC 92 +ea q+rgW++eiv+++s lv+v+p+g+lkCvDgR+sd++r+ gpk++Gg++aia+nrgv+++egl+qitkev++kGh p+vHgd+++++lgC 3BOBA 7 AEAlQGRGWDAEIVTDASmagqLVDVRPEGILKCVDGRGSDNTRMGGPKMPGGIYAIAHNRGVTSIEGLKQITKEVASKGHLPSVHGDHSSDMLGC 102 67889**********9999***************************************************************************** PP domain1.fasta 93 GffklwltgkladvglprpefsaeelaeiveeaggvveelkGkHeekvvvlNfvpgtTlepnaedqrFvvDaWaadklgldveklleaaaatVelL 188 Gffklw+tg+++d+g+prp+f+a+++a++v+ agg +e+++G+H+ekvv++N+ +++Tlepn++dqrF+vD+Waadk+gldv+k+l aaaatVe+L 3BOBA 103 GFFKLWVTGRFDDMGYPRPQFDADQGANAVKDAGGIIEMHHGSHTEKVVYINLLANKTLEPNENDQRFIVDGWAADKFGLDVPKFLIAAAATVEML 198 ************************************************************************************************ PP domain1.fasta 189 sgpkiaki 196 +gpk+aki 3BOBA 199 GGPKNAKI 206 ******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (196 nodes) Target sequences: 180940 (47973432 residues) Passed MSV filter: 4609 (0.0254725); expected 3618.8 (0.02) Passed bias filter: 3739 (0.0206643); expected 3618.8 (0.02) Passed Vit filter: 249 (0.00137615); expected 180.9 (0.001) Passed Fwd filter: 5 (2.76335e-05); expected 1.8 (1e-05) Initial search space (Z): 180940 [actual number of targets] Domain search space (domZ): 5 [number of targets reported over threshold] # CPU time: 2.28u 0.08s 00:00:02.36 Elapsed: 00:00:00.66 # Mc/sec: 14246.66 //