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= 0001.3877.p (395 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313277|ref|YP_003777369.1| branched-chain amino acid ABC t... 729 0.0 gi|300313292|ref|YP_003777384.1| branched-chain amino acid ABC t... 427 e-120 gi|300312955|ref|YP_003777047.1| amino acid ABC transporter peri... 101 1e-22 gi|300313931|ref|YP_003778023.1| branched-chain amino acid ABC t... 75 8e-15 gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC t... 75 9e-15 >gi|300313277|ref|YP_003777369.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 395 Score = 729 bits (1881), Expect = 0.0, Method: Compositional matrix adjust. Identities = 366/395 (92%), Positives = 379/395 (95%) Query: 1 MMSEMINTHRRHLMLAGSALAAGALPLLARAADAVKVGLIVPMSGPFASTGRQIEAAVKL 60 MMSEMINT RR +MLAG+AL AG P+LARAAD +KVGLIVPMSGPFASTGRQIEAAVKL Sbjct: 1 MMSEMINTRRRQVMLAGTALVAGGAPMLARAADVLKVGLIVPMSGPFASTGRQIEAAVKL 60 Query: 61 YQQKYGESVAGRKVEILLKDDGGVSPDVTKRLAQELVARDKAQVLMGFGLTPLALAAAPI 120 YQQKYG+SVAGRKVEI+LKDDGGVSPDVTKRLAQELV+R+KAQVLMGFGLTPLALAAAPI Sbjct: 61 YQQKYGDSVAGRKVEIVLKDDGGVSPDVTKRLAQELVSREKAQVLMGFGLTPLALAAAPI 120 Query: 121 ATQAKVPMIVTAAATSIIPQRSPFIVRTGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGP 180 ATQAK PMIVTAAATSIIPQRSP+IVRTGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGP Sbjct: 121 ATQAKAPMIVTAAATSIIPQRSPYIVRTGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGP 180 Query: 181 GLDAEKVFVKNFSEAGGKVMESVRVPLRNPDYAPFLQRVKDAKPEALFVFVPSGEGAAVL 240 GLDAEKVFVK F EAGGKVMESVRVPLRNPDYAPFLQRVKDAKP+ALFVFVPSGEGAAVL Sbjct: 181 GLDAEKVFVKTFGEAGGKVMESVRVPLRNPDYAPFLQRVKDAKPQALFVFVPSGEGAAVL 240 Query: 241 KQFTERGLGAAGIRLICTGDVLDDDLMAGIGAAAKDVVSSHHYSAAHPSAANKEYVESIA 300 KQFTERGL AAGIRLICTGDVLDDDLMAGIGAAAKDVVSSHHYSAAHPSAANKEYVE++A Sbjct: 241 KQFTERGLAAAGIRLICTGDVLDDDLMAGIGAAAKDVVSSHHYSAAHPSAANKEYVEAMA 300 Query: 301 KANKGMRANFHSVGAYDGMHLLYESLKKTGGDADGGKLLAVMKGMSWESVRGPVTIDAAT 360 KANKGMRANFHSVGAYDGMHLLYESLKKTGGDADG KLLA MKGMSWESVRGPV +DAAT Sbjct: 301 KANKGMRANFHSVGAYDGMHLLYESLKKTGGDADGDKLLAAMKGMSWESVRGPVAVDAAT 360 Query: 361 RDIVQTVYMRKAELRGTEFYNVEFDQVVNVRDPGV 395 RDIVQTVYMRKAELRG EFYNVEFDQV VRDPGV Sbjct: 361 RDIVQTVYMRKAELRGAEFYNVEFDQVEKVRDPGV 395 >gi|300313292|ref|YP_003777384.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 391 Score = 427 bits (1097), Expect = e-120, Method: Compositional matrix adjust. Identities = 209/387 (54%), Positives = 278/387 (71%), Gaps = 2/387 (0%) Query: 10 RRHLMLAGSALAAGALPLLARAADAVKVGLIVPMSGPFASTGRQIEAAVKLYQQKYGESV 69 ++ +LA A + G L LA+A + +KVGLI SGPFA G+Q+E +K Y ++G+ V Sbjct: 4 KKIALLAVMAASGGLLASLAQAQETIKVGLIAAFSGPFADYGKQMEGGIKAYMAQHGDQV 63 Query: 70 AGRKVEILLKDDGGVSPDVTKRLAQELVARDKAQVLMGFGLTPLALAAAPIATQAKVPMI 129 AG+K++I++KD G SP++ KRLAQELV R+K L GFGLTP ALA APIA QAK PMI Sbjct: 64 AGKKIQIIIKDTTGPSPEIAKRLAQELVVREKVDFLAGFGLTPEALAVAPIAEQAKKPMI 123 Query: 130 VTAAATSIIPQRSPFIVRTGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGPGLDAEKVFV 189 + AATS+I +S +I R TL QV+ P+A+WA KNGIK VVT V+DYGPG+DAE F Sbjct: 124 IMNAATSVITTKSNYIARFSMTLPQVSGPMATWALKNGIKRVVTLVADYGPGIDAETAFK 183 Query: 190 KNFSEAGGKVMESVRVPLRNPDYAPFLQRVKDAKPEALFVFVPSGEGA-AVLKQFTERGL 248 N GG+V+ES+RVPLRNP++AP++QR+KDAKPEA+F+FVP+GE + A +K + ERGL Sbjct: 184 TNLLGGGGQVLESIRVPLRNPEFAPYIQRIKDAKPEAVFIFVPAGEQSIAFMKGYRERGL 243 Query: 249 GAAGIRLICTGDVLDDDLMAGIGAAAKDVVSSHHYSAAHPSAANKEYVESIAKANKGM-R 307 AGI++I TGD+ DD +M +G + V+++ HYSAAH S NK +++S A AN G R Sbjct: 244 AEAGIKVIATGDLTDDHVMPAMGESTLGVITTFHYSAAHDSPENKAFLKSFAAANPGAGR 303 Query: 308 ANFHSVGAYDGMHLLYESLKKTGGDADGGKLLAVMKGMSWESVRGPVTIDAATRDIVQTV 367 NF +V AYDGM+ +YE KK G DG + +A++K M + S RGP+ ID ATRDIVQTV Sbjct: 304 PNFMAVAAYDGMNAIYEVSKKLNGKIDGDRAMAILKTMKFTSPRGPIAIDPATRDIVQTV 363 Query: 368 YMRKAELRGTEFYNVEFDQVVNVRDPG 394 Y+RK E G E YNVEFD+ N++D G Sbjct: 364 YVRKVEKIGNEAYNVEFDKFENMKDTG 390 >gi|300312955|ref|YP_003777047.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 392 Score = 101 bits (251), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 97/355 (27%), Positives = 162/355 (45%), Gaps = 12/355 (3%) Query: 19 ALAAGALPLLARAADAVKVGLIVPMSGPFASTGRQIEAAVKLYQQKYGESVAGRKVEILL 78 A+A GA L A+AAD VKVG + +SGP ++ G L + G + G E+++ Sbjct: 14 AMAVGA-SLPAQAADVVKVGFLTTLSGPASAPGVDEREGFMLALKTLGNKLGGVPAEVIV 72 Query: 79 KDDGGVSPDVTKRLAQELVARDKAQVLMGFGLTPLALAAAPIATQAKVPMIVTAAATSII 138 DD SPD K+ A L+ R+K +L GF + + LA AP A +K ++ A + + Sbjct: 73 VDD-QFSPDAAKQGADRLIKREKVDILSGFVYSNILLAVAPAAFASKTVVVSANAGPAQL 131 Query: 139 PQR--SPFIVRTGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGPGLDAEKVFVKNFSEAG 196 +P+ + A G + V +Y G DA F K F + Sbjct: 132 AGAGCNPYFFSASYQNDAAHEAAGKLMADKGYQRVAIIAPNYPAGKDASAGF-KRFLKKD 190 Query: 197 GKVMESVRVPLRNPDYAPFLQRVKDAKPEALFVFVPSGEGAAVLKQFTERGLGAAGIRLI 256 V + L D+A + +++ A +AL+ F+P G G +KQ+ G+ +R++ Sbjct: 191 PAV--ELFPKLGQLDFATEIAQLRAANIDALYFFLPGGMGVNFVKQYAAAGMDPKIVRVM 248 Query: 257 CTGDVLDDDLMAGIGAAAKDVVSSHHYSAAHPSAANKEYVESIAKANKGMRANFHSVGAY 316 D D M G V ++ +S+ P+ N+ +V + K G + + + AY Sbjct: 249 PAYDA--DQQMLSNGDLIAGVANTGQWSSDLPNEQNRAFVAAYLK-EYGRQPSMFASQAY 305 Query: 317 DGMHLLYESLKKTGGDADGGK-LLAVMKGMSWESVRGPVTIDAATRDIVQTVYMR 370 D L+ ++K GG + + L+A +K +++SVRG AA +Q Y R Sbjct: 306 DAAMLIDSAVKAVGGKVENREALIAAIKTANFKSVRGGFRF-AANHFPIQNQYAR 359 >gi|300313931|ref|YP_003778023.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 397 Score = 75.1 bits (183), Expect = 8e-15, Method: Compositional matrix adjust. Identities = 96/375 (25%), Positives = 158/375 (42%), Gaps = 19/375 (5%) Query: 10 RRHLMLAGSALAAGALPL--LARAADAVKVGLIVPMSGPFASTGRQIEAAVKLYQQKYGE 67 RRH + + A GAL + A+++ G VPMSGPFA+ G+ + +KL QKYG+ Sbjct: 4 RRHFLKLSALAAPGALSYHDVFAQAESIAFGCPVPMSGPFAANGKFADLGMKLALQKYGK 63 Query: 68 SVAGRKVEILLKDDGGVSPDVTKRLAQELVARDKAQVLMGFGLTPLALAAAPIATQAKVP 127 V G+ + D G P R QE + + + G L+ ALA A +A Sbjct: 64 -VLGKSTSYVNLDTEG-KPATAVRKMQESIEKG-TRFFAGGILSGEALAMGKEADKAGAV 120 Query: 128 MIVTAAATSII---PQRSPF--IVRTGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGPGL 182 I TA A I R+ F V T + Q PL +T +G GL Sbjct: 121 FITTAGADEITGSDCNRATFRWSVPTFGAIEQTVRPLLEKMPNAKRWYTITPQYVFGEGL 180 Query: 183 DAEKVFVKN-FSEAGGKVMESVRVPLRNPDYAPFLQRVKDAKPEALFVFVPSGEGAAVLK 241 + KN F E G + + + L +++ +L AKP+ L + + + L+ Sbjct: 181 LSA---AKNIFKEKGIEHVGNSYHSLTEKEFSGYLTNAIAAKPDVLLLLNFGSQSSDTLR 237 Query: 242 QFTERGLGAAGIRLICTGDVLDDDLMAGIGAAAKD-VVSSHHYSAAHPSAANKEYVESIA 300 Q G+ L+ L+ +GA D V Y A + NKE+V+ + Sbjct: 238 QAVSFGMKNNCTILMAWASGLEQ--FETLGADICDGVYFGAQYWHAIDAPFNKEFVK-LV 294 Query: 301 KANKGMRANFHSVGAYDGMHLLYESLKKTGGDADGGKLLAVMKGMSWESVRGPVTIDAAT 360 N + N+ G+Y ++ +++ K D ++A M+GM +E + G I Sbjct: 295 NDNLKIDPNYSLAGSYICTKIILDAIIK-ANSTDPKAVIAAMEGMKYEGLTGSEEIRKGD 353 Query: 361 RDIVQTVYMRKAELR 375 +++ Y+ K + + Sbjct: 354 HQVIKNYYLLKGKAK 368 >gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 75.1 bits (183), Expect = 9e-15, Method: Compositional matrix adjust. Identities = 61/236 (25%), Positives = 106/236 (44%), Gaps = 4/236 (1%) Query: 16 AGSALAAGALPLLARAADAVKVGLIVPMSGPFAS-TGRQIEAAVKLYQQKYGESVAGRKV 74 A + L A LP A D +K+G I MSG +A G+ A+++ G ++ G+KV Sbjct: 14 ACALLGAAILPSAQAAGDTIKIGFITDMSGTYADFDGQGGVEAIRMAIADAGGAINGKKV 73 Query: 75 EILLKDDGGVSPDVTKRLAQELVARDKAQVLMGFGLTPLALAAAPIATQAKVPMIVTAAA 134 E++ D D+ A+E RD +L+G + +LA +A + K I A Sbjct: 74 ELVFADHQN-KADIAANKAREWFDRDGVDMLVGGVNSAASLAMGKVAGEKKKVFISVGAG 132 Query: 135 TS--IIPQRSPFIVRTGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGPGLDAEKVFVKNF 192 T+ + + + ++ + + + + G KS +DY G EK + Sbjct: 133 TTRQTNEECNAYTIQYAYDTTALARGTGAAITRQGGKSWYFLTADYAFGTSLEKDTSEVV 192 Query: 193 SEAGGKVMESVRVPLRNPDYAPFLQRVKDAKPEALFVFVPSGEGAAVLKQFTERGL 248 GG V+ + RVPL D++ FL + + +K + L + V G+ +K E G+ Sbjct: 193 KSNGGNVVGATRVPLATSDFSSFLLQAQSSKAQILGLAVAGGDVINAIKAANEFGV 248 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 0.318 0.133 0.377 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: 1,074,293 Number of extensions: 41501 Number of successful extensions: 174 Number of sequences better than 1.0e-08: 16 Number of HSP's gapped: 161 Number of HSP's successfully gapped: 16 Length of query: 395 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 308 Effective length of database: 1,207,925 Effective search space: 372040900 Effective search space used: 372040900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 131 (55.1 bits)