# 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_598.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_598 [L=290] Description: # 663602 # 664471 # 1 # ID=1_598;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.261 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-26 92.8 0.6 3e-26 92.3 0.6 1.2 1 Peripla_BP_2 Periplasmic binding protein ------ inclusion threshold ------ 0.11 12.6 0.7 0.24 11.5 0.7 1.6 1 DUF3847 Protein of unknown function (DUF3847) 5.5 6.9 7.4 0.4 10.6 0.7 2.3 3 DUF4446 Protein of unknown function (DUF4446) Domain annotation for each model (and alignments): >> Peripla_BP_2 Periplasmic binding protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 92.3 0.6 5.4e-30 3e-26 1 234 [. 30 261 .. 30 264 .. 0.88 Alignments for each domain: == domain 1 score: 92.3 bits; conditional E-value: 5.4e-30 EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-B-BESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS- CS Peripla_BP_2 1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellksgip 84 i+sl+ s +e+ll+l +++++g +++ + + + ++++ e + E l l PDl+i+ l + ++ g++ 23726_FusoPortal_Gene_598 30 IVSLTLSGDEMLLGLVPENRIAGLSGKINEDKEISNIV-DKAKKFPKVEGNEEVLMSLEPDLIIVADWL-SKRITDIGAITGAK 111 89999999999999955555666555555555554443.555555566888899***********9888.66666666779*** PP EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHT--TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHT CS Peripla_BP_2 85 tvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdllda 166 ++++ + n e+ k+ ir l+ l+++++++ekl++ +d++l a++++i++ ++kp ++++++ + + +g n+ ++d++ 23726_FusoPortal_Gene_598 112 VYFYKTPNSYEEQKKLIRDLANLVEEKENGEKLIKNMDDRLKALQNKIAKNykGAKPRILMYTSFS---TTSGKNTTFNDMVKL 192 ********99********************************************************...*************** PP S--EES-TT--STT-EEE-HHHHHHH--SEEEEEEH.HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS Peripla_BP_2 167 lgieniaaeskkseyeeisaEqilasdpdvifvsgr.aeadnktgleflkenpllaelpAvkngrVyal 234 +++ n+ ae + +++++is E + + +pd+i+v + ++ +++ + + e+p +++++A+kn++Vy + 23726_FusoPortal_Gene_598 193 INGVNVVAEAGIDGFKDISKEKVIELNPDIIIVPIAkKYDNVNKISKLFFEDPSFKNVKAIKNKKVYFI 261 ******88877*************************8788899999*********************87 PP >> DUF3847 Protein of unknown function (DUF3847) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.5 0.7 4.3e-05 0.24 2 36 .. 131 165 .. 130 169 .. 0.90 Alignments for each domain: == domain 1 score: 11.5 bits; conditional E-value: 4.3e-05 DUF3847 2 leeLkqelekaekkleqaehrekiLenrkkklekg 36 l++L +e+e++ek ++++ r+k L+n+++k kg 23726_FusoPortal_Gene_598 131 LANLVEEKENGEKLIKNMDDRLKALQNKIAKNYKG 165 67899***********************9998766 PP >> DUF4446 Protein of unknown function (DUF4446) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.7 0.1 0.43 2.4e+03 9 28 .. 6 25 .. 3 40 .. 0.59 2 ? 10.6 0.7 7.2e-05 0.4 33 96 .. 117 182 .. 110 187 .. 0.88 3 ? -1.3 0.1 0.32 1.8e+03 23 55 .. 249 281 .. 222 288 .. 0.52 Alignments for each domain: == domain 1 score: -1.7 bits; conditional E-value: 0.43 DUF4446 9 lvvillillivllvklkklk 28 l++ill+ + ++++k ++k 23726_FusoPortal_Gene_598 6 LFIILLFSFTIVNAKGVQVK 25 45555555555555544443 PP == domain 2 score: 10.6 bits; conditional E-value: 7.2e-05 DUF4446 33 klmkgkdgksleellkekleeveelkeeneelekrieeleeklkkslq..kvglvrYdAFeemGgd 96 + + +++k+l + l++ +ee e+ ++ +++++r+++l++k++k+++ k +++ Y F+ ++g+ 23726_FusoPortal_Gene_598 117 TPNSYEEQKKLIRDLANLVEEKENGEKLIKNMDDRLKALQNKIAKNYKgaKPRILMYTSFSTTSGK 182 5556678999999********************************99755889*******998886 PP == domain 3 score: -1.3 bits; conditional E-value: 0.32 DUF4446 23 klkklkkkykklmkgkdgksleellkekleeve 55 ++k +k+k +++ kd + + + + +ee+ 23726_FusoPortal_Gene_598 249 NVKAIKNKKVYFIQYKDITPTSQYMINSIEELA 281 344444444444444444444444444444444 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (290 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1190 (0.0712063); expected 334.2 (0.02) Passed bias filter: 631 (0.0377573); expected 334.2 (0.02) Passed Vit filter: 64 (0.00382958); 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: 0.26u 0.23s 00:00:00.49 Elapsed: 00:00:00.31 # Mc/sec: 2719.48 // [ok]