# 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_384.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_384 [L=310] Description: # 421090 # 422019 # -1 # ID=1_384;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.286 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-84 281.8 13.2 6.3e-84 281.6 13.2 1.0 1 ABC_sub_bind ABC transporter substrate binding protein 2.3e-09 37.1 6.7 0.00074 19.1 0.3 3.0 3 Peripla_BP_4 Periplasmic binding protein domain ------ inclusion threshold ------ 0.061 13.3 0.0 0.22 11.6 0.0 1.9 1 DUF2325 Uncharacterized protein conserved in bacteria ( Domain annotation for each model (and alignments): >> ABC_sub_bind ABC transporter substrate binding protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.6 13.2 1.1e-87 6.3e-84 1 289 [. 26 306 .. 26 309 .. 0.98 Alignments for each domain: == domain 1 score: 281.6 bits; conditional E-value: 1.1e-87 EEEEEES---HHHHHHHHHHHHHHHHTT--BTTTEEEEEEE-TT-HHHHHHHHHHHHTT--SEEEEESHHHHHHHHHH-SSS-E CS ABC_sub_bind 1 kiavaqfvehdaldaivkGikdaLkdkgveegknvlykvknaegdqskvaqiirqlkaekpdlivgiatpaaqilksatkniPi 84 k++++q+veh++lda++kG+++aLk+kg +gkn+++++++a+gd +++ i++ +k+d+iv+i+tp+aq++ +atk+iPi 23726_FusoPortal_Gene_384 26 KVGITQIVEHPSLDATRKGVEKALKEKG--KGKNIKIEYQSAQGDFGTAQLIAKSYSSSKKDVIVAISTPSAQAALNATKTIPI 107 79*************************9..567*************************************************** PP EEEEES-TTTTTS-S-SSS--SSEEEEE----HHHHHHHHHHHSTT--EEEEEE-TT-HHHHHHHHHHHHHHHHTT-EEEEEE- CS ABC_sub_bind 85 VfaavtdpvgakLvksleapgenvTGvsdaekvektieLikkllPnvkkigilyspgeansvslveelkklakkaglkvveaav 168 V +avtd +a+L g+n+TG sd+++++k+ eLik llPn+kk+g ly+p+e+ns+ l e++k++ak++gl+vve v 23726_FusoPortal_Gene_384 108 VYTAVTDGASAGL------KGNNITGTSDMSPLDKQAELIKTLLPNAKKVGFLYNPSEQNSLLLLEKFKRIAKAKGLTVVEKGV 185 **********998......468************************************************************** PP SSGGGHHHHHHHHHTT-SEEEE-S-HHHHHTHHHHHHHHHHTT--EEESSHHHHHTT-SEEEE--HHHHHHHHHHHHHHHHTT- CS ABC_sub_bind 169 knvndvesavsslaekvdaiyiltdnliasafeavvkaanqakiPviasddesvkegalaalgvnekelGvqagkvvvkiLkGk 252 +vnd++ a+ sl ++ d++yi+tdnl+ s + v+++an++ +Pvias +++v++gala ++++ lG+q+g+ v+ +L+Gk 23726_FusoPortal_Gene_384 186 SSVNDINLAIDSLLGQIDVLYIPTDNLVYSSASLVIQKANKKNVPVIASTNDIVEKGALATESIDYEKLGYQTGERVIDVLNGK 269 ************************************************************************************ PP -GGGS--EE----EEEE-HHHHHHTT----HHHHHH- CS ABC_sub_bind 253 kpkdipvsrakslklvinkkaakelgitikeellksa 289 +pkdipv++ k+ +lvin+k+ak+ +i +++ lk a 23726_FusoPortal_Gene_384 270 NPKDIPVETLKQTTLVINQKIAKKYNISLDNPKLKNA 306 ****************************998888776 PP >> Peripla_BP_4 Periplasmic binding protein domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 15.0 1.3 2.2e-06 0.012 130 241 .. 30 135 .. 17 144 .. 0.78 2 ! 5.8 0.0 0.0015 8.2 111 195 .. 137 213 .. 135 218 .. 0.87 3 ! 19.1 0.3 1.3e-07 0.00074 72 123 .. 220 273 .. 211 294 .. 0.87 Alignments for each domain: == domain 1 score: 15.0 bits; conditional E-value: 2.2e-06 TSCCCHHHHHHHHHHHHHHHHH-TTCEECC.EEESTTTCHHHHHHHHHHHHHTTTECEEEESSCCHHHCHHHHHHHTTTTSTEE CS Peripla_BP_4 130 aGspgdpnaeeriegfrkvlkeypgikiva.evaganwdaekaqqalealltanpldgilaandgmaegalealeaaglagkvv 212 + +p + +g++k+lke+++ k ++ e++ a+ d +aq + ++ + ++ d+i+a ++ a++al+a++ + 23726_FusoPortal_Gene_384 30 TQIVEHPSLDATRKGVEKALKEKGKGKNIKiEYQSAQGDFGTAQLIAKSYSSSKK-DVIVAISTPSAQAALNATKT------IP 106 4667788888899*********55555555577899****************663.89999999999988888888......33 PP EEEES-HHHHHHHHHTTSSEEEEE--HHH CS Peripla_BP_4 213 vtgqDatpealeaikdGtidatvaqdpye 241 ++ +t+ a + +k +i++t +p + 23726_FusoPortal_Gene_384 107 IVYTAVTDGASAGLKGNNITGTSDMSPLD 135 88888888888888888888888888865 PP == domain 2 score: 5.8 bits; conditional E-value: 0.0015 HHHHHHHHCTTH.EEEEEETSCCCHHHHHHHHHHHHHHHHH-TTCEECCEEESTTTCHHHHHHHHHHHHHTTTECEEEESSCCH CS Peripla_BP_4 111 qaeylaeklggkkgkvvilaGspgdpnaeeriegfrkvlkeypgikivaevaganwdaekaqqalealltanpldgilaandgm 194 qae+++ l++ +kv l +p+ +n+ + +e f+ + k+ +g+++v++ + + ++ + a+++ll ++d+ + + d+ 23726_FusoPortal_Gene_384 137 QAELIKTLLPNA-KKVGFL-YNPSEQNSLLLLEKFKRIAKA-KGLTVVEK---GVSSVNDINLAIDSLLG--QIDVLYIPTDNL 212 89********99.999988.9*****************999.99999994...46899999999999999..488888888876 PP H CS Peripla_BP_4 195 a 195 + 23726_FusoPortal_Gene_384 213 V 213 5 PP == domain 3 score: 19.1 bits; conditional E-value: 1.3e-07 HHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HHHHHHHHHHHHHHHCTTH.... CS Peripla_BP_4 72 alkkakaaGIpVvafdsddapsgerlayvgfdneaaGelqaeylaeklggk...k 123 +++ka+++++pV+a d +++ la ++d e+ G++ +e + + l+gk + 23726_FusoPortal_Gene_384 220 VIQKANKKNVPVIASTND-IVEKGALATESIDYEKLGYQTGERVIDVLNGKnpkD 273 8*****************.******************************997543 PP >> DUF2325 Uncharacterized protein conserved in bacteria (DUF2325) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.6 0.0 3.9e-05 0.22 38 80 .. 192 235 .. 165 242 .. 0.78 Alignments for each domain: == domain 1 score: 11.6 bits; conditional E-value: 3.9e-05 DUF2325 38 k.kleskigkaDlvvlftdtvsHkavkkvkkeakkkgkpvvrlh 80 + ++s +g+ D++ ++td + ++ v ++a+kk++pv+ + 23726_FusoPortal_Gene_384 192 NlAIDSLLGQIDVLYIPTDNLVYSSASLVIQKANKKNVPVIAST 235 25899***********************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (310 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 667 (0.0399114); expected 334.2 (0.02) Passed bias filter: 420 (0.0251316); expected 334.2 (0.02) Passed Vit filter: 30 (0.00179512); 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: 0.25u 0.23s 00:00:00.48 Elapsed: 00:00:00.32 # Mc/sec: 2816.19 // [ok]