# 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_723.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_723 [L=148] Description: # 816736 # 817179 # 1 # ID=1_723;partial=00;start_type=ATG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp;gc_cont=0.257 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-26 91.5 1.4 5.3e-26 91.2 1.4 1.0 1 ExbD Biopolymer transport protein ExbD/TolR ------ inclusion threshold ------ 0.049 14.0 0.1 0.24 11.8 0.0 1.9 2 SecD-TM1 SecD export protein N-terminal TM region 0.1 12.8 0.0 0.12 12.5 0.0 1.2 1 Beta-Casp Beta-Casp domain Domain annotation for each model (and alignments): >> ExbD Biopolymer transport protein ExbD/TolR # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 91.2 1.4 9.5e-30 5.3e-26 8 127 .. 16 142 .. 11 145 .. 0.94 Alignments for each domain: == domain 1 score: 91.2 bits; conditional E-value: 9.5e-30 ExbD 8 inltpmiDvvflLLifFlvtaklkkpeplevdlPsssstqkeveekelirisisadgsiy.........ldkkavsveelaqkl 82 +++tp+iDvvflLLifF++++++++ ++ ++dlP+s++ ++ ++ +++++ +++d+++y + +++++ ++ + 23726_FusoPortal_Gene_723 16 LEITPLIDVVFLLLIFFMLATSFDERSAFKIDLPKSTAAKT-KSTLKEVQVLVDKDKNVYlrytdnsgkSQNEKLDLTSFVSVV 98 789************************99***********5.9999**********9999899999888888889********* PP ExbD 83 kerkakppdkltvaikadkdvsygklvevldtlkkagiekvslvt 127 e+ +++++k v+i+adk++ yg +ve+++ lk+ g +++++ t 23726_FusoPortal_Gene_723 99 SEKLNNSENK-DVIISADKNIDYGFIVEIMSLLKESGASAINIDT 142 **********.*****************************99866 PP >> SecD-TM1 SecD export protein N-terminal TM region # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.8 0.0 4.3e-05 0.24 11 60 .. 21 70 .. 19 88 .. 0.88 2 ? -0.1 0.0 0.21 1.2e+03 33 65 .. 109 138 .. 91 145 .. 0.73 Alignments for each domain: == domain 1 score: 11.8 bits; conditional E-value: 4.3e-05 SecD-TM1 11 lilvvlligllyalPnlygedpavqisaakatlkvdeatlskveqaLkea 60 li vv+l++++++l + + e +a +i k+t++ +++tl++v+ ++ 23726_FusoPortal_Gene_723 21 LIDVVFLLLIFFMLATSFDERSAFKIDLPKSTAAKTKSTLKEVQVLVDKD 70 5779999************************************9888765 PP == domain 2 score: -0.1 bits; conditional E-value: 0.21 SecD-TM1 33 avqisaakatlkvdeatlskveqaLkeagievk 65 v isa k ++d +++ ++ + Lke+g ++ 23726_FusoPortal_Gene_723 109 DVIISADK---NIDYGFIVEIMSLLKESGASAI 138 45555555...4688888899999998887665 PP >> Beta-Casp Beta-Casp domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.5 0.0 2.2e-05 0.12 41 81 .. 77 128 .. 28 139 .. 0.66 Alignments for each domain: == domain 1 score: 12.5 bits; conditional E-value: 2.2e-05 G.............SHH.....HHHH..HHHS-SSEEEEES-TTSSSSHHHHHHH CS Beta-Casp 41 y.............aks.lewmeskkeelnsskgpkvilassgmlegGrsrellk 81 y +s ++ +++k ln+s++ vi++++ +++G+++e++ 23726_FusoPortal_Gene_723 77 YtdnsgksqnekldLTSfVSVVSEK---LNNSENKDVIISADKNIDYGFIVEIMS 128 2333444433333312223333333...45788999***************9976 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (148 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 964 (0.0576831); expected 334.2 (0.02) Passed bias filter: 507 (0.0303375); expected 334.2 (0.02) Passed Vit filter: 38 (0.00227382); expected 16.7 (0.001) Passed Fwd filter: 3 (0.000179512); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.23u 0.24s 00:00:00.47 Elapsed: 00:00:00.32 # Mc/sec: 1344.50 // [ok]