# 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_163.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_163 [L=469] Description: # 172749 # 174155 # -1 # ID=1_163;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.242 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-09 37.4 0.3 6.1e-09 35.8 0.3 1.9 1 HTH_17 Helix-turn-helix domain ------ inclusion threshold ------ 0.056 13.5 0.2 0.17 11.9 0.1 1.9 2 MerR_1 MerR HTH family regulatory protein 0.066 12.9 0.0 0.16 11.7 0.0 1.6 1 MerR MerR family regulatory protein 0.1 12.2 0.0 0.43 10.1 0.0 2.0 2 Hfq Hfq protein Domain annotation for each model (and alignments): >> HTH_17 Helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 35.8 0.3 1.5e-12 6.1e-09 1 40 [. 118 158 .. 118 159 .. 0.95 Alignments for each domain: == domain 1 score: 35.8 bits; conditional E-value: 1.5e-12 HTH_17 1 lltveEaAelLgvsrstvyrlirrgelpaak.iGrryripr 40 +l+veE A+ +v+++tv+++irrg+++ ak iGr ++i++ 23726_FusoPortal_Gene_163 118 YLSVEEYAKVYDVKPTTVRQWIRRGKIRNAKkIGRDWLISE 158 89****************************66*******85 PP >> MerR_1 MerR HTH family regulatory protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.9 0.1 4.1e-05 0.17 2 30 .. 120 148 .. 119 154 .. 0.88 2 ? -3.5 0.0 2.5 1.1e+04 47 62 .. 442 457 .. 442 458 .. 0.87 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 4.1e-05 EHHHHHHHHTS-HHHHHHHHHHTT-S-EE CS MerR_1 2 sigevakilgvtthtlrywekegllkpkr 30 s+ e ak v++ t+r w ++g+++ ++ 23726_FusoPortal_Gene_163 120 SVEEYAKVYDVKPTTVRQWIRRGKIRNAK 148 78899*******************99877 PP == domain 2 score: -3.5 bits; conditional E-value: 2.5 HHHHHHHHTT--GGG- CS MerR_1 47 klikyLlkrGltlkgi 62 k++k +l++G ++++i 23726_FusoPortal_Gene_163 442 KKVKVFLENGWKIRNI 457 689999**99999988 PP >> MerR MerR family regulatory protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.7 0.0 3.9e-05 0.16 6 26 .. 125 145 .. 120 149 .. 0.86 Alignments for each domain: == domain 1 score: 11.7 bits; conditional E-value: 3.9e-05 HHHHTTTHHHHHHHHHTTSST CS MerR 6 AeltGvsprtLRyYEreGLip 26 A+ +v p t+R + r+G+i+ 23726_FusoPortal_Gene_163 125 AKVYDVKPTTVRQWIRRGKIR 145 8899***************95 PP >> Hfq Hfq protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.3 0.0 0.76 3.2e+03 34 44 .. 204 214 .. 202 217 .. 0.80 2 ? 10.1 0.0 0.0001 0.43 5 27 .. 433 455 .. 431 466 .. 0.87 Alignments for each domain: == domain 1 score: -2.3 bits; conditional E-value: 0.76 -SSEEEEEETT CS Hfq 34 DnfvvlLesdg 44 D++ +lL+s++ 23726_FusoPortal_Gene_163 204 DKYEILLSSKK 214 9******8875 PP == domain 2 score: 10.1 bits; conditional E-value: 0.0001 HHHHHHHTT-EEEEEETTS-EEE CS Hfq 5 fLnqlrkekipvtifLvnGiklk 27 fL + +ke +v++fL nG k++ 23726_FusoPortal_Gene_163 433 FLLEWQKESKKVKVFLENGWKIR 455 89999***************986 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (469 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 861 (0.0515199); expected 334.2 (0.02) Passed bias filter: 337 (0.0201652); expected 334.2 (0.02) Passed Vit filter: 44 (0.00263284); expected 16.7 (0.001) Passed Fwd filter: 4 (0.000239349); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.27u 0.23s 00:00:00.50 Elapsed: 00:00:00.31 # Mc/sec: 4398.06 // [ok]