# 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_1215.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1215 [L=724] Description: # 1319343 # 1321514 # -1 # ID=1_1215;partial=00;start_type=GTG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.275 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-69 234.1 2.1 3.1e-69 233.4 2.1 1.3 1 Transpeptidase Penicillin binding protein transpeptidase dom 6.1e-12 46.1 9.4 1.2e-11 45.2 7.2 2.3 2 PBP_dimer Penicillin-binding Protein dimerisation domai 1.1e-06 28.3 0.2 3.1e-06 26.8 0.2 1.9 1 PASTA PASTA domain 0.0064 15.9 7.3 0.01 15.2 7.3 1.3 1 YibE_F YibE/F-like protein ------ inclusion threshold ------ 4.7 5.3 10.6 7.9 4.5 10.6 1.3 1 DUF2070 Predicted membrane protein (DUF2070) Domain annotation for each model (and alignments): >> Transpeptidase Penicillin binding protein transpeptidase domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 233.4 2.1 9.3e-73 3.1e-69 4 305 .. 328 628 .. 325 629 .. 0.91 Alignments for each domain: == domain 1 score: 233.4 bits; conditional E-value: 9.3e-73 EEEETTT-BEEEEEEESE-TTTHHCCTCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSSTTSEEEEETCCEETTSS..ECTC CS Transpeptidase 4 vvldaktgevlamaskpsydpnakvgkneplanravqsqyePGStfKvvtaaaaleagvikpdetlddsggkiqggqs.ikdw 85 +++d+++g++la a +d ++ l+n +qsqyePGS+fK++++aaa+++++i++++ ++ +gki+ + i++ 23726_FusoPortal_Gene_1215 328 LIMDPNNGKILAVAAFS-KD-------KNLLRNNIFQSQYEPGSIFKPLIVAAAMNEKFINENTAFNVGDGKIKRFKKtIRES 402 79************995.44.......34678999*************************************99844334444 PP CCC-SSSSEE.EHHHHHHTT-HHHHHHHHHHH-HHHHHHHHHHTTTTS-SSSSSTT-B--B--S..SH..HHHHHHHHTTTSB CS Transpeptidase 86 eqdnkgsegi.tlrealekSsntyfvklaqklgadklrkylkkfglGnktgidlpgesaGvptr..kw..legatisfgiGlt 163 ++ +gi t re+++kSsn+++v +++ +++ylk+fgl ktg+d+p+e + + + +w l+++ ++fg+G+ 23726_FusoPortal_Gene_1215 403 SRS---TRGIiTAREVVMKSSNVGMVLISDYFTNALFEDYLKAFGLYDKTGVDFPNELKPYTSSykNWdgLKKNNMAFGQGVV 482 444...46677***********************************************9977664455*************** PP B-HHHHHHHHHHHHTTTEEE--BSEEEEEECTT.EEEESS-EEEEE-S-HHHHHHHHHHHHHHHHCTTTTGCGTCTTS--EEE CS Transpeptidase 164 vtplqlaqayaaiangGklvkPhlvkaivdpdg.vrkvkpkelnklpisketaekvkeglkgvvsrgsgtataavegykvagK 245 +tp+q+++a++a++ngG+l+kP++v++i+d++g v++ +++ +++is+e +ek++ +l++ v++g+g+ + +egy v gK 23726_FusoPortal_Gene_1215 483 ITPIQMITAFSAVVNGGTLYKPYIVEKITDSEGtVIMRNTPTAVRKVISEEVSEKMRSILEDTVEKGTGKRAY-IEGYAVGGK 564 **********************************9********************************777777.********* PP EEEEEECSSSTTSEEEEEEEEEEEEEESTTS-SEEEEEEECTCS.....SSSSCCHHHHHHHHHH CS Transpeptidase 246 TGTAevagkkgngkkegakiswfvgyapadnpkyavavlieqpk.....eaaggkaaapiakkil 305 TGTA+ +++g+ +++ s+f+g+ pad+pky+v+ +++ p+ ++ gg +aap++ +i+ 23726_FusoPortal_Gene_1215 565 TGTAQLSA-GKSGYIRNEYLSSFIGFFPADKPKYIVMAMFMRPQadiqaNKFGGVVAAPVVGNII 628 ******98.5566777789*****************************99***********9997 PP >> PBP_dimer Penicillin-binding Protein dimerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 45.2 7.2 3.5e-15 1.2e-11 4 158 .. 107 262 .. 104 266 .. 0.87 2 ? -0.2 0.0 0.31 1e+03 8 37 .. 509 538 .. 509 548 .. 0.86 Alignments for each domain: == domain 1 score: 45.2 bits; conditional E-value: 3.5e-15 E----EE-TTS-EEEEEEEEEEEEEE--SS--HHHHHH.HHHHHCCH.HHHS---HHHHHHHCHHHHTS-TT-EESTTSSEET CS PBP_dimer 4 apRGeIyDrngrlLAtnrpsytltitpsklkkkkalek.ikkLakll.eseenldderleelalkknsykaykpvviaedise 84 ++RG IyD +g+ LA n+ +yt++i+ps l+++k ++ +k+++ + ++ +l+d+ le+ k +s ++++ + +di++ 23726_FusoPortal_Gene_1215 107 GQRGLIYDNKGKKLAFNNRKYTISINPSLLNDEKIHDEiVKDIVAIRdSKIVKLEDNILEK-LSKLASEGNRYKR-LVKDIDD 187 68********************************999999999999988778888877777.4444444444444.4467*** PP CCHHHHHHHGGG............STT-EEEEEEEEEETTSSTTHHHH-EEEEC.HHHHHHHHCHTTSTCEEEEECHHHHHTH CS PBP_dimer 85 eevarikenakd............lpGinievepkRyYpkgelaahvlGyvgkiteeelekykekgyssgdliGksGlEkqyE 155 e+ ++i e + +++e++ +R+Y k++ + +++G v + s++++ G sGlEkqy 23726_FusoPortal_Gene_1215 188 EQKEQIDELLAGiertkvkgspkyRTVLQFEKSIERKYYKQDEYEKLIGMVRFT-----------EESRDERLGISGLEKQYQ 259 *********99999******99977778999********************999...........7899************** PP HHH CS PBP_dimer 156 eeL 158 ++L 23726_FusoPortal_Gene_1215 260 NYL 262 999 PP == domain 2 score: -0.2 bits; conditional E-value: 0.31 -EE-TTS-EEEEEEEEEEEEEE--SS--HH CS PBP_dimer 8 eIyDrngrlLAtnrpsytltitpsklkkkk 37 +I D++g+++ n+p+ +++ +++++k 23726_FusoPortal_Gene_1215 509 KITDSEGTVIMRNTPTAVRKVISEEVSEKM 538 699************999999988887765 PP >> PASTA PASTA domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 26.8 0.2 9.4e-10 3.1e-06 2 61 .. 670 722 .. 669 723 .. 0.96 Alignments for each domain: == domain 1 score: 26.8 bits; conditional E-value: 9.4e-10 E--TTTTSBHHHHHHHHHHTT--ECEEEEEE-CCGCTCEEEECS-TTSEEETTS-EEEEE CS PASTA 2 tvPdvtGmsvdeAkatLkalGlkiktveetsddvpeGtVisQsPeaGtevskgskvtltv 61 +Pd+ Gms e+ a k+ ++ + + +++G V +Q P+aG ++++ +kv++++ 23726_FusoPortal_Gene_1215 670 VMPDLEGMSPQEVLAVFKETNI-------DIEVIGTGLVEEQRPAAGDSLKNVKKVKILL 722 6*********************.......***********************99**9976 PP >> YibE_F YibE/F-like protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 15.2 7.3 3.1e-06 0.01 31 114 .. 12 96 .. 5 114 .. 0.79 Alignments for each domain: == domain 1 score: 15.2 bits; conditional E-value: 3.1e-06 YibE_F 31 llvlilvl.lplllkgvspllvalllvilitvvtlllvngfnkktlaallgtllgvllalllallviklakltGlnseeaeel 112 +l+++l + l++++ ll+ +l++i+ +v+++ +++ + kk l a ++++ ++++++l+++ ++l++++ l++++ l 23726_FusoPortal_Gene_1215 12 FLLFVLGVsGYLIYNKSFFLLTLFLFSIVYLVFSIAVISNWGKKQLFAKRSSIMLLIILFFLIVYGLRLLGIQYLQKSKYVAL 94 44444444356777888889999999***********************************************9987776444 PP YibE_F 113 ly 114 ++ 23726_FusoPortal_Gene_1215 95 MN 96 33 PP >> DUF2070 Predicted membrane protein (DUF2070) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 4.5 10.6 0.0024 7.9 16 103 .. 5 93 .. 2 103 .. 0.61 Alignments for each domain: == domain 1 score: 4.5 bits; conditional E-value: 0.0024 DUF2070 16 vsllliillalligllaflssk..lfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivviisllaillsal 95 + ++ i++l +++g+ +l+++ +f + lf++ +v++++ v++ g++ l krs ++ l++++++++ l + + + 23726_FusoPortal_Gene_1215 5 IKIAGILFLLFVLGVSGYLIYNksFFLLTLFLF-SIVYLVFSIAVISNWGKKqLFAKRSSIMLLIILFFLIVYGLRLLGIQY- 85 556666666677676666666543344444444.4555555555555555555999***99999999998886555555554. PP DUF2070 96 lqalvlla 103 lq++ + a 23726_FusoPortal_Gene_1215 86 LQKSKYVA 93 44444444 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (724 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1119 (0.0669579); expected 334.2 (0.02) Passed bias filter: 501 (0.0299785); expected 334.2 (0.02) Passed Vit filter: 56 (0.00335089); expected 16.7 (0.001) Passed Fwd filter: 5 (0.000299186); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 5 [number of targets reported over threshold] # CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.33 # Mc/sec: 6377.85 // [ok]