BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0001.3403.p (405 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312743|ref|YP_003776835.1| membrane-fusion protein [Herbas... 734 0.0 gi|300311362|ref|YP_003775454.1| HlyD family secretion, possible... 169 5e-43 gi|300309820|ref|YP_003773912.1| acriflavin resistance lipoprote... 61 2e-10 gi|300313894|ref|YP_003777986.1| RND family efflux transporter M... 60 3e-10 gi|300310689|ref|YP_003774781.1| RND family efflux transporter M... 60 4e-10 >gi|300312743|ref|YP_003776835.1| membrane-fusion protein [Herbaspirillum seropedicae SmR1] Length = 402 Score = 734 bits (1894), Expect = 0.0, Method: Compositional matrix adjust. Identities = 368/391 (94%), Positives = 378/391 (96%) Query: 1 MTEPHDPLPHIVPTTHTPARQKMWGSALALVLVLGGGYWLYSRQQPVPPAAKPIPVKLET 60 MTEPHDPLPHIVPTTH P RQK W S++ALV+VLGGGYWLYSRQQP PPA KPIPVKLET Sbjct: 1 MTEPHDPLPHIVPTTHAPTRQKAWWSSVALVIVLGGGYWLYSRQQPPPPAPKPIPVKLET 60 Query: 61 VTVERADLEQVVNATGNVVAQDYVDVGSKVAGQISDVDVVIGETVKAGRLLATVAPAVQS 120 VTVERADLEQVVNATGNVVAQDYVDVGSKVAGQISDVDVV+GETVKAG+LLATVAPAVQS Sbjct: 61 VTVERADLEQVVNATGNVVAQDYVDVGSKVAGQISDVDVVVGETVKAGKLLATVAPAVQS 120 Query: 121 SRIESNRATLARLKAELAGQNAQLDFAQLQFQRQTQLKAENATREESYESSRMNMAAAAS 180 SRIE+NRATLARLKAELAGQNAQLDFAQLQFQRQTQLKAENATREESYESSRMNM AAA+ Sbjct: 121 SRIENNRATLARLKAELAGQNAQLDFAQLQFQRQTQLKAENATREESYESSRMNMYAAAA 180 Query: 181 RVDATNAQIQQTEAAIREDEAVQKQTRIEAPANGTIVTLNARPGQMVGANQEVLMRIADL 240 RVDATNAQIQQTEAAIREDEAVQKQTRIEAP +GTIVTLNARPGQMV ANQE LMRIADL Sbjct: 181 RVDATNAQIQQTEAAIREDEAVQKQTRIEAPVSGTIVTLNARPGQMVAANQEALMRIADL 240 Query: 241 SRMTVQVPVAEEDVTRLQKGMTAYFTTPGYPGKRWSGKLRQIMLLPTDDSGRQGKKAYYT 300 SRMTVQVPVAEEDVTRLQKGMTAYFTTPGYPGKRWSGKLRQIMLLPTDDSGRQGKKA+YT Sbjct: 241 SRMTVQVPVAEEDVTRLQKGMTAYFTTPGYPGKRWSGKLRQIMLLPTDDSGRQGKKAFYT 300 Query: 301 VLFDVANPSRELMSGMSADVYFVLARAEHVPTIPRTLVTKPGMDGTQTVKVVLADGTLES 360 V FDVANPSRELMSGMSADVYFVLARAEHVPTIPRTLVTKPGMDGTQTVKVVLADG LE+ Sbjct: 301 VFFDVANPSRELMSGMSADVYFVLARAEHVPTIPRTLVTKPGMDGTQTVKVVLADGKLET 360 Query: 361 RKIKIGIRDGERAQVLSGLKEGEQVLLPANP 391 RKIKIGIRD ERAQVLSGLKEGEQVLLPANP Sbjct: 361 RKIKIGIRDNERAQVLSGLKEGEQVLLPANP 391 >gi|300311362|ref|YP_003775454.1| HlyD family secretion, possible efflux component [Herbaspirillum seropedicae SmR1] Length = 407 Score = 169 bits (427), Expect = 5e-43, Method: Compositional matrix adjust. Identities = 115/355 (32%), Positives = 182/355 (51%), Gaps = 25/355 (7%) Query: 53 PIPVKLETVTVERADLEQVVNATGNVVAQDYVDVGSKVAGQISDVDVVIGETVKAGRLLA 112 P P + T AD++ VV A+G V A V VG++V+GQI + V +G+ VK G+L+A Sbjct: 35 PAPPTYLSATARVADIQDVVLASGTVKAYKQVSVGAQVSGQIKSLKVALGDQVKKGQLVA 94 Query: 113 TVAPAVQSSRIESNRATLARLKAELAGQNAQLDFAQLQFQRQTQLKAENATREESYESSR 172 + Q++ + S +L L+A+L + A L AQL + RQ + A +A+ E++ES+ Sbjct: 95 EIDSLTQANALASAEFSLQNLQAQLRAKEASLKQAQLAYARQKMMLAGDASSRENFESAE 154 Query: 173 MNMAAAASRVDATNAQIQQTEAAIREDEAVQK--QTRIEAPANGTIVTLNARPGQMVGAN 230 + + + A AQI+ + AI+ D A TRI +P G +V + A+ GQ V AN Sbjct: 155 ATLNTTQADIAALQAQIK--DGAIKVDTARLNLGYTRISSPIEGQVVAIVAQEGQTVNAN 212 Query: 231 QE--VLMRIADLSRMTVQVPVAEEDVTRLQKGMTAYFTTPGYPGKRWSGKLRQIMLLPTD 288 Q ++++A + +T++ ++E DV R++ G +FT G P R+ LR I P Sbjct: 213 QSTPTIIKVARMDTVTIKAQISEADVVRVKPGQPVFFTILGDPDHRYRTTLRAIE--PAP 270 Query: 289 DSGRQGK-----------------KAYYTVLFDVANPSRELMSGMSADVYFVLARAEHVP 331 DS Q YY L DV NP +L M+ V VL+ A + Sbjct: 271 DSILQDDTSSSTTSITSSSSASSTAIYYNGLLDVPNPDGKLRISMTTQVNIVLSEASNAL 330 Query: 332 TIPRTLVTKPGMDGTQTVKVVLADGTLESRKIKIGIRDGERAQVLSGLKEGEQVL 386 +P T + DG+ TV+V+ G RK++IGI Q++ G+K GE+V+ Sbjct: 331 VLPSTALGAKAADGSYTVRVLDDQGQAHERKVRIGINTNALVQIVEGVKAGERVV 385 >gi|300309820|ref|YP_003773912.1| acriflavin resistance lipoprotein A [Herbaspirillum seropedicae SmR1] Length = 402 Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 89/329 (27%), Positives = 136/329 (41%), Gaps = 42/329 (12%) Query: 76 GNVVAQDYVDVGSKVAGQISDVDVVIGETVKAGRLLATVAPAVQSSRIESNRATLARLKA 135 G V A V ++VAG + G VK G++L + PA + +ES +ATLAR +A Sbjct: 57 GRVEAFRVAQVRARVAGIVQKRVFKEGSEVKEGQVLFKIDPAQYKASLESAQATLARAQA 116 Query: 136 ELAGQNAQLDFAQLQFQRQTQLKAENATREESYESSRMNMAAAASRVDATNAQIQQTEAA 195 L L QR L NA ++ Y+++ A + V A A +Q A+ Sbjct: 117 NLTQTT-------LTAQRYKPLVEVNAVSKQEYDNAVAAQKQAEADVAAGKAAVQ--TAS 167 Query: 196 IREDEAVQKQTRIEAPANGTIVTLNARPGQMVGANQEV-LMRIADLSRMTVQVPVAEEDV 254 + A + +P +G I G +VG L + L + V V + D+ Sbjct: 168 LNLGYAT-----VTSPISGRIGRALVTEGALVGQGDATQLALVQQLDPVYVNVTQSSADL 222 Query: 255 TRLQKGMTA-YFTTPG---------------YPGKRWSGKLRQIMLLPTDDSGRQGKKAY 298 +LQ+ M A + G YP GKL + +++G +A Sbjct: 223 LKLQQAMAAGQLKSVGDNKASVTLELENGQAYP---LPGKLLFSDISVDENTGSVSLRAE 279 Query: 299 YTVLFDVANPSRELMSGMSADVYFVLARAEHVPTIPRTLVTKPGMDGTQTVKVVLADGTL 358 + NP R L+ G A E +P+ V + G TV VV A+ + Sbjct: 280 FP------NPKRLLLPGTYVRAKIEQAVDEQALLVPQQAVVRDA--GGSTVMVVNAENKV 331 Query: 359 ESRKIKIGIRDGERAQVLSGLKEGEQVLL 387 E R +K G G QVL GLKEG++V++ Sbjct: 332 EPRPVKTGGARGNNWQVLDGLKEGDRVIV 360 >gi|300313894|ref|YP_003777986.1| RND family efflux transporter MFP subunit [Herbaspirillum seropedicae SmR1] Length = 428 Score = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 103/399 (25%), Positives = 163/399 (40%), Gaps = 54/399 (13%) Query: 13 PTTHTPARQKMWGSA---LALVLVLGGGYWLYSRQQPVPPAAKPIPVKLETVTVERADLE 69 PT TP RQ SA LAL L+L SR P V V +R L Sbjct: 3 PTASTPRRQGRTSSATARLALSLILVAVLAACSRSGDQPKPTAQAEVGYVVVKAQRQAL- 61 Query: 70 QVVNATGNVVAQDYVDVGSKVAGQISDVDVVIGETVKAGRLLATVAPAVQSSRIESNRAT 129 G A D+ +V G I G TVKAG+ L + PA + +S RA+ Sbjct: 62 -TTELPGRTTAYLAADIRPQVGGIIQKRLFKEGSTVKAGQPLYQIDPASYQAAYDSARAS 120 Query: 130 LARLKAELAGQNAQLDFAQLQFQRQTQLKAENATREESYESSRMNMAAAASRVDATNAQI 189 L LKAE A L ++L+ +R +L +A ++ + ++ + + V+ A + Sbjct: 121 L--LKAE-----ATLASSKLKAERYAELNKIDAVSKQDNDDAQSTLRQNQADVEVQKAAV 173 Query: 190 QQTEAAIREDEAVQKQTRIEAPANGTIVTLNARPGQMVGANQEV-LMRIADLSRMTVQVP 248 Q AAI + T+I +P +G I PG +V A+Q L + + + V V Sbjct: 174 Q--TAAIN-----LQYTKILSPISGRIEKSAVTPGALVTASQTTALTTVQQIDPIYVDVT 226 Query: 249 VAEEDVTRLQKGMTAYFTTPGYPGKRWSGKLR-------QIMLLPTDDSG--RQGKKAYY 299 + D+ RL++ + SG++R Q+ ++ D S R GK + Sbjct: 227 QSTVDLLRLRRELA-------------SGQIRKSGENAAQVKIVLEDGSTYERPGKLEFT 273 Query: 300 TVLFD-----------VANPSRELMSGMSADVYFVLARAEHVPTIPRTLVTKPGMDGTQT 348 + D V NP L+ G +H P+ V++ G T Sbjct: 274 GLSVDTGTGMITLRAVVPNPDGVLLPGAYVRAVLEEGVDDHALLAPQKAVSRD-QTGAAT 332 Query: 349 VKVVLADGTLESRKIKIGIRDGERAQVLSGLKEGEQVLL 387 V+ ADG ++ R + + G V GLKEG+++++ Sbjct: 333 ALVLGADGKVQQRLVSVARAVGNNWWVSRGLKEGDKLIV 371 >gi|300310689|ref|YP_003774781.1| RND family efflux transporter MFP subunit [Herbaspirillum seropedicae SmR1] Length = 400 Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 88/342 (25%), Positives = 143/342 (41%), Gaps = 32/342 (9%) Query: 58 LETVTVERADLEQVVNATGNVVAQDYVDVGSKVAGQISDVDVVIGETVKAGRLLATVAPA 117 L VTV +E G DV +V G I G VKAG++L + PA Sbjct: 41 LGVVTVHAQPVELHTELPGRTSPYQIADVRPQVNGIIKARSFREGSDVKAGQVLYQINPA 100 Query: 118 VQSSRIESNRATLARLKAELAGQNAQLDFAQLQFQRQTQLKAENATREESYESSRMNMAA 177 + +S+ A LA KAE A + A+L+ R +L A A ++ Y+ + ++ Sbjct: 101 SYQAAYDSSVAALA--KAE-----ASVRTARLKASRYKELVAIKAVSQQDYDDAVASLGE 153 Query: 178 AASRVDATNAQIQQTEAAIREDEAVQKQTRIEAPANGTIVTLNARPGQMVGANQEV-LMR 236 A + V + A +Q + I D A R++AP +G I + PG +V ANQ L Sbjct: 154 AEADVGSARANVQTSR--INLDYA-----RLDAPISGRIGKSSVTPGALVTANQTTALTT 206 Query: 237 IADLSRMTVQVPVAEEDVTRLQKGMTAYFTTPGYPGKRWSGKLRQIMLLPTDDSGRQGKK 296 I L + V V + L++ + G K +G +++L ++G Sbjct: 207 IQQLDPIYVDVTQSSTTWLNLKEALAN-----GQLEKSGNGAKVRLVLENGRTYAQEGTL 261 Query: 297 AYYTVLFD-----------VANPSRELMSGMSADVYFVLARAEHVPTIPRTLVTKPGMDG 345 + V + NP +L+ GM + +P+ V++ G G Sbjct: 262 QFSDVTVNQDTGAITLRAIFPNPKTDLLPGMYVRAVLQEGVRQQGLLVPQQAVSRDGA-G 320 Query: 346 TQTVKVVLADGTLESRKIKIGIRDGERAQVLSGLKEGEQVLL 387 VV A G +E R + G++ V SGLKEG+Q+++ Sbjct: 321 KPVAFVVNAQGVVEQRALVTDRAIGDQWLVSSGLKEGDQLVV 362 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.314 0.129 0.360 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,130,199 Number of extensions: 42930 Number of successful extensions: 157 Number of sequences better than 1.0e-08: 11 Number of HSP's gapped: 149 Number of HSP's successfully gapped: 11 Length of query: 405 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 318 Effective length of database: 1,207,925 Effective search space: 384120150 Effective search space used: 384120150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 132 (55.5 bits)