-------------------------------------------------------------------------------- Domain name : PF00482.15_GSPII_F Domain size : 77 Domain Description : Bacterial type II secretion system protein F domain Domain gathering score : 17.8 Domain trusted cutoff : 17.9 Domain architecture : non-TM/SP [1 165], TM [166 185] -------------------------------------------------------------------------------- Example 1 gi|70726732|ref|YP_253646.1| hypothetical protein SH1731 [Staphylococcus haemolyticus JCSC1435]gi|68447456|dbj|BAE05040.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435] 442 (length) 157 196 .. (wrt seq) 135 185 .] (wrt HMM) No.of residues in non-TM/SP region : 31 [19%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- FtsQ Cell division protein FtsQ 88.4 2.6e-23 1 POTRA_1 POTRA domain, FtsQ-type 64.6 3.3e-18 1 GSPII_F Bacterial type II secretion system pr 18.0 0.00044 1 Surf_Ag_VNR Surface antigen variable number repea 15.7 0.0014 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- GSPII_F 1/1 157 196 .. 97 136 .] 18.0 0.00044 POTRA_1 1/1 198 266 .. 1 74 [] 64.6 3.3e-18 Surf_Ag_VNR 1/1 198 266 .. 1 84 [] 15.7 0.0014 FtsQ 1/1 269 391 .. 1 131 [] 88.4 2.6e-23 Alignments of top-scoring domains: GSPII_F: domain 1 of 1, from 157 to 196: score 18.0, E = 0.00044 *->dllrerresrrqllagllypllllivallilllllaillp<-* ++++e+++++r++++ +++++++ +++lli+l+ll +++p gi|7072673 157 QERKEQLRIQRRKRQKRIQYVIITFLVLLIILFLLYMFTP 196 POTRA_1: domain 1 of 1, from 198 to 266: score 64.6, E = 3.3e-18 *->fpikeveVsGdnkrvsaeeirkalgiqksdgtsffsldlnairdrLe ++i+++++sG n++vs+ +++kal ++ ++ + + ++ + ++L+ gi|7072673 198 SRISNIKISG-NNNVSNSQVEKALDVKD--NSRMYTYSKRKGIQNLK 241 kklPWiksasVrrqLwPntleIrvvEr<-* k + +ik++++++q +Pntl+++++E gi|7072673 242 K-NDLIKDVKIKKQ-LPNTLKVQITEN 266 Surf_Ag_VNR: domain 1 of 1, from 198 to 266: score 15.7, E = 0.0014 *->ykikvdInieGNwalkrtsdevLrrellklkeGdvynrekleedier +i+ +I+i+GN + +s ++++++l +k ++ ++ i++ gi|7072673 198 SRIS-NIKISGN---NNVSNSQVEKAL-DVKDNSRMYTYSKRKGIQN 239 LkdfYlnlGYafadVsvepe.dpekdggVdltfnVkEg<-* Lk ++ dV+++ + + +l++ ++E+ gi|7072673 240 LK----KNDL-IKDVKIKKQlPN------TLKVQITEN 266 FtsQ: domain 1 of 1, from 269 to 391: score 88.4, E = 2.6e-23 *->vAyWqqkggglylidenGevfsaplasraappdLPllvGpegaekav v+++ + ++++ +i e + ++ +++ + P+l G++g+ek gi|7072673 269 VGVV-KEKNKYVPIIEGNQELKN--FDGNIAGSGPILEGFKGEEK-- 310 lellkllnallpplglrvselvlsptrrrWdlvLdyMndGirvkLgredp +++k l++++p++++++se+ + p+ +++++L+yM+d+++v+ ++ ++ gi|7072673 311 SNMIKSLSKMSPEIRDMISEIKYAPKQNSPNRILLYMQDDMQVVGNIKTI 360 aderlqrfaalypqlllkleknknkrgiayvDLR<-* a +++++++++ ++l k++++++ + y+DL gi|7072673 361 A-NKIKYYPQMSQSL-SKDDSGNL-KTQGYIDLS 391 Example 2 gi|120599464|ref|YP_964038.1| methyl-accepting chemotaxis sensory transducer [Shewanella sp. W3-18-1]gi|124547313|ref|ZP_01706244.1| methyl-accepting chemotaxis sensory transducer [Shewanella putrefaciens 200]gi|146292538|ref|YP_001182962.1| methyl-accepting chemotaxis sensory transducer [Shewanella putrefaciens CN-32]gi|120559557|gb|ABM25484.1| methyl-accepting chemotaxis sensory transducer [Shewanella sp. W3-18-1]gi|124509315|gb|EAY53396.1| methyl-accepting chemotaxis sensory transducer [Shewanella putrefaciens 200]gi|145564228|gb|ABP75163.1| methyl-accepting chemotaxis sensory transducer [Shewanella putrefaciens CN-32] 540 (length) 157 206 .. (wrt seq) 125 185 .] (wrt HMM) No.of residues in non-TM/SP region : 41 [25%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- MCPsignal Methyl-accepting chemotaxis protein ( 221.2 2.7e-63 1 HAMP HAMP domain 58.0 2.5e-15 1 GSPII_F Bacterial type II secretion system pr 17.6 0.00055 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- GSPII_F 1/1 157 206 .. 87 136 .] 17.6 0.00055 HAMP 1/1 191 260 .. 1 79 [] 58.0 2.5e-15 MCPsignal 1/1 284 540 .] 1 288 [] 221.2 2.7e-63 Alignments of top-scoring domains: GSPII_F: domain 1 of 1, from 157 to 206: score 17.6, E = 0.00055 *->nlseaLerladllrerresrrqllagllypllllivallilllllai ++s+a+++lad+ +er ++++ ++ +++++l+ ++a++++ ++ a+ gi|1205994 157 KVSNAISALADYQQERSLVEANSAKHTIELALSTMIAIVVFAVIGAV 203 llp<-* +l+ gi|1205994 204 VLA 206 HAMP: domain 1 of 1, from 191 to 260: score 58.0, E = 2.5e-15 CS HHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXXXXXX.XXXXXX *->lllvllialllalllalllarrilrPlrrLaeaarriasGtdLdvri +++++++a++ a++la++++r+++ P ++ ++ +riasG dL+ gi|1205994 191 MIAIVVFAVIGAVVLAYFFSRSLIGPMQNAVAICQRIASG-DLT--- 233 CS XXXXX.........XXXXXXXXXXXXXXXXXX esgrdrvlpvsgpDEigeLarafNqMaerLre<-* + + + DE g+++r++ M+++L++ gi|1205994 234 ----QKF-ADDAADEAGDMIRSMAVMQQQLQQ 260 MCPsignal: domain 1 of 1, from 284 to 540: score 221.2, E = 2.7e-63 CS -----HHHHHH..............HHHHHHHHHHHHHHHHH...HH *->eeqAsaieQvANGaedQierIEtaeasleqltATvreiAsNAEDVaq ++ + Q + E a+++ +lt + e+A+ A + gi|1205994 284 DQSSQTLHQQS-------QELELAATAVTELTTAIEEVARSA---SA 320 CS HHHHHHHHTTTH..............HHHHHHTTTHHHHHHHHHHHHHHH AsdlAkqAseeAdeGgKevanvvdemsqigqevddavqvveeLatssknI +s +++A+ +A G+ v + +++++ e+++a q + +La ++++I gi|1205994 321 TSSDSETANIKARQGKERVQHTIQTIQTLEGELQQARQGIQQLASRVNEI 370 CS HHHHHHHHHHHHHHHHHHHHHHHHHHHTG..GGGHHHHHHHHHHHHHHHH sdIisVIdeIAfQTNLLALNAAIEAARAGGNEqGRGFAVVAdEVRkLAer s++++VI++IA+QTNLLALNAAIEAARAG E GRGFAVVAdEVR+LA r gi|1205994 371 SSVLDVIRGIAEQTNLLALNAAIEAARAG--ESGRGFAVVADEVRALAHR 418 CS HHHHHHHHHHHHHHHHHH..............HHHHHHHHHHTTTTTTSH SAqaAkEIeqLIeeivkesndavesmektrtevevGveivekTgealkeI +++++kEIe +++e+ + v m+ ++ +++ i++++g+al+ I gi|1205994 419 TQESTKEIERMMHLVQAETQTTVNTMQNSSNRATETLLIAQQAGDALQQI 468 CS HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHH.... veaiaeiadevqeIAaaseEQSagieqinDsFAqaveridqvTqqnsAHi ++aia+i+ ++ IA+a+eEQ++++ ++ ++ i +++ q+ gi|1205994 469 ATAIAQINEQNLTIASAAEEQATVAREVD----GNLLNIRDLSHQT---- 510 CS ..........HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT rdiAAlaEEQaalveEasaAsesLseqAeeLtalvaqFklk<-* +a + E a+s+ L ++Ae L lv +Fk gi|1205994 511 ----------SAGAHETQASSADLARLAETLNSLVTSFK-V 540