# hmmscan :: search sequence(s) against a profile database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: AA/23726_FusoPortal_Gene_1638.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1638 [L=415] Description: # 1756346 # 1757590 # 1 # ID=1_1638;partial=00;start_type=TTG;rbs_motif=GGAGG;rbs_spacer=5-10bp;gc_cont=0.264 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-59 198.6 0.0 9.8e-59 197.5 0.0 1.6 1 YkuD_2 L,D-transpeptidase catalytic domain ------ inclusion threshold ------ 1.4 8.8 8.0 2.3 8.2 8.0 1.3 1 RP-C_C Replication protein C C-terminal region Domain annotation for each model (and alignments): >> YkuD_2 L,D-transpeptidase catalytic domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.5 0.0 1.2e-62 9.8e-59 3 169 .] 58 222 .. 56 222 .. 0.99 Alignments for each domain: == domain 1 score: 197.5 bits; conditional E-value: 1.2e-62 YkuD_2 3 eklskealekalkgleklkkkkkekkkltiiDfskpStekRlfviDlkkkkllletlvahGknsgenlatkFsneegSkkssl 85 +k+++++++ka+ g+ ++++k+ l+iiD+skpS+e+R++v+Dl+kkkl+++t vah knsg ++ +Fs++++S++ssl 23726_FusoPortal_Gene_1638 58 NKIDYSIFQKAYLGYVQISNKNPGV--LIIIDYSKPSNEERFYVLDLDKKKLVYSTRVAHSKNSGLEIPLEFSDDPNSYQSSL 138 799********************99..******************************************************** PP YkuD_2 86 GlyktgetykgkhGlslrLeGlekgiNdnAreRaivlHgadyvseelikklgrlgrSlGCpavseelakkiiellkegsllfi 168 G+++t +y+g+ G+slrL+Gle++iN nA++Raiv+Hg d+v++e+ikk g +grSlGCp+++++l+++ii+ +k+g++lfi 23726_FusoPortal_Gene_1638 139 GFFVTLGEYNGAYGYSLRLKGLEENINANAEDRAIVIHGGDIVEDEYIKKFGFAGRSLGCPVLPHSLTREIIDFIKHGRVLFI 221 *********************************************************************************** PP YkuD_2 169 y 169 y 23726_FusoPortal_Gene_1638 222 Y 222 9 PP >> RP-C_C Replication protein C C-terminal region # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.2 8.0 0.00028 2.3 25 100 .. 327 403 .. 305 413 .. 0.71 Alignments for each domain: == domain 1 score: 8.2 bits; conditional E-value: 0.00028 RP-C_C 25 leelleelealreevenal.esalkaenssanesqnerhiqnsnpdsssesepasekereekeaaaasaeaepsekk 100 l+++++e + +e+++++ +++ ++en++ +e++ e+ i++ +p+ + e e +++e+ ++++++++++p+e + 23726_FusoPortal_Gene_1638 327 LKDVIQEKLNKITEIKETTeNKKINDENMDNKEKAVEQTITDNTPETKKEDETVVIQQNENVQEDKKEERKHPEEVT 403 55555555555677777775677899999999*************98888886555555555555555555554443 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (415 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 3022 (0.180828); expected 334.2 (0.02) Passed bias filter: 545 (0.0326113); expected 334.2 (0.02) Passed Vit filter: 57 (0.00341072); expected 16.7 (0.001) Passed Fwd filter: 2 (0.000119674); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.31 # Mc/sec: 3891.67 // [ok]