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= 0001.3894.p (391 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313292|ref|YP_003777384.1| branched-chain amino acid ABC t... 753 0.0 gi|300313277|ref|YP_003777369.1| branched-chain amino acid ABC t... 402 e-113 gi|300312955|ref|YP_003777047.1| amino acid ABC transporter peri... 107 1e-24 gi|300314071|ref|YP_003778163.1| amino acid ABC transporter peri... 84 2e-17 gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC t... 83 4e-17 >gi|300313292|ref|YP_003777384.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 391 Score = 753 bits (1945), Expect = 0.0, Method: Compositional matrix adjust. Identities = 367/391 (93%), Positives = 383/391 (97%) Query: 1 MSFKKIALLALISATNALAAPLAQAEDTIKVGLIAAFSGPFADYGKQMEGGIKAYMAQHG 60 M FKKIALLA+++A+ L A LAQA++TIKVGLIAAFSGPFADYGKQMEGGIKAYMAQHG Sbjct: 1 MRFKKIALLAVMAASGGLLASLAQAQETIKVGLIAAFSGPFADYGKQMEGGIKAYMAQHG 60 Query: 61 DQVAGKKVQVIIKDTTGPSPEIAKRLAQELVVRDKVDFLAGFGLTPEALAVAPIAEQAKK 120 DQVAGKK+Q+IIKDTTGPSPEIAKRLAQELVVR+KVDFLAGFGLTPEALAVAPIAEQAKK Sbjct: 61 DQVAGKKIQIIIKDTTGPSPEIAKRLAQELVVREKVDFLAGFGLTPEALAVAPIAEQAKK 120 Query: 121 PMIIMNAASSIITTKSNYIARFSMTLPQVSGPMATWALKNGIKRVVTLVADYGPGIDAET 180 PMIIMNAA+S+ITTKSNYIARFSMTLPQVSGPMATWALKNGIKRVVTLVADYGPGIDAET Sbjct: 121 PMIIMNAATSVITTKSNYIARFSMTLPQVSGPMATWALKNGIKRVVTLVADYGPGIDAET 180 Query: 181 AFKTNLLGGGGEVVESIRVPLRNPEFAPYIQRIKDAKPQAVFIFVPAGEQSIAFMKGYRE 240 AFKTNLLGGGG+V+ESIRVPLRNPEFAPYIQRIKDAKP+AVFIFVPAGEQSIAFMKGYRE Sbjct: 181 AFKTNLLGGGGQVLESIRVPLRNPEFAPYIQRIKDAKPEAVFIFVPAGEQSIAFMKGYRE 240 Query: 241 RGLAEAGIKVIATGDLTDDHVMPAMGDSTLGVITTFHYSAAHDSPENKAFLKSFAAANPD 300 RGLAEAGIKVIATGDLTDDHVMPAMG+STLGVITTFHYSAAHDSPENKAFLKSFAAANP Sbjct: 241 RGLAEAGIKVIATGDLTDDHVMPAMGESTLGVITTFHYSAAHDSPENKAFLKSFAAANPG 300 Query: 301 AGRPNFMAVAAYDGMNAIYEVSKKLNGKIDGERAMAILKTMKFVSPRGPIAIDPATRDIV 360 AGRPNFMAVAAYDGMNAIYEVSKKLNGKIDG+RAMAILKTMKF SPRGPIAIDPATRDIV Sbjct: 301 AGRPNFMAVAAYDGMNAIYEVSKKLNGKIDGDRAMAILKTMKFTSPRGPIAIDPATRDIV 360 Query: 361 QTVYVRKVEKIGKEAYNVEFDKFENMKDTGK 391 QTVYVRKVEKIG EAYNVEFDKFENMKDTGK Sbjct: 361 QTVYVRKVEKIGNEAYNVEFDKFENMKDTGK 391 >gi|300313277|ref|YP_003777369.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 395 Score = 402 bits (1034), Expect = e-113, Method: Compositional matrix adjust. Identities = 205/369 (55%), Positives = 269/369 (72%), Gaps = 2/369 (0%) Query: 22 LAQAEDTIKVGLIAAFSGPFADYGKQMEGGIKAYMAQHGDQVAGKKVQVIIKDTTGPSPE 81 LA+A D +KVGLI SGPFA G+Q+E +K Y ++GD VAG+KV++++KD G SP+ Sbjct: 28 LARAADVLKVGLIVPMSGPFASTGRQIEAAVKLYQQKYGDSVAGRKVEIVLKDDGGVSPD 87 Query: 82 IAKRLAQELVVRDKVDFLAGFGLTPEALAVAPIAEQAKKPMIIMNAASSIITTKSNYIAR 141 + KRLAQELV R+K L GFGLTP ALA APIA QAK PMI+ AA+SII +S YI R Sbjct: 88 VTKRLAQELVSREKAQVLMGFGLTPLALAAAPIATQAKAPMIVTAAATSIIPQRSPYIVR 147 Query: 142 FSMTLPQVSGPMATWALKNGIKRVVTLVADYGPGIDAETAFKTNLLGGGGEVVESIRVPL 201 TL QV+ P+A+WA KNGIK VVT V+DYGPG+DAE F GG+V+ES+RVPL Sbjct: 148 TGFTLAQVTAPLASWAAKNGIKSVVTFVSDYGPGLDAEKVFVKTFGEAGGKVMESVRVPL 207 Query: 202 RNPEFAPYIQRIKDAKPQAVFIFVPAGEQSIAFMKGYRERGLAEAGIKVIATGDLTDDHV 261 RNP++AP++QR+KDAKPQA+F+FVP+GE + A +K + ERGLA AGI++I TGD+ DD + Sbjct: 208 RNPDYAPFLQRVKDAKPQALFVFVPSGEGA-AVLKQFTERGLAAAGIRLICTGDVLDDDL 266 Query: 262 MPAMGDSTLGVITTFHYSAAHDSPENKAFLKSFAAANPDAGRPNFMAVAAYDGMNAIYEV 321 M +G + V+++ HYSAAH S NK ++++ A AN R NF +V AYDGM+ +YE Sbjct: 267 MAGIGAAAKDVVSSHHYSAAHPSAANKEYVEAMAKANKGM-RANFHSVGAYDGMHLLYES 325 Query: 322 SKKLNGKIDGERAMAILKTMKFVSPRGPIAIDPATRDIVQTVYVRKVEKIGKEAYNVEFD 381 KK G DG++ +A +K M + S RGP+A+D ATRDIVQTVY+RK E G E YNVEFD Sbjct: 326 LKKTGGDADGDKLLAAMKGMSWESVRGPVAVDAATRDIVQTVYMRKAELRGAEFYNVEFD 385 Query: 382 KFENMKDTG 390 + E ++D G Sbjct: 386 QVEKVRDPG 394 >gi|300312955|ref|YP_003777047.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 392 Score = 107 bits (268), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 104/352 (29%), Positives = 161/352 (45%), Gaps = 15/352 (4%) Query: 23 AQAEDTIKVGLIAAFSGPFADYGKQMEGGIKAYMAQHGDQVAGKKVQVIIKDTTGPSPEI 82 AQA D +KVG + SGP + G G + G+++ G +VI+ D SP+ Sbjct: 23 AQAADVVKVGFLTTLSGPASAPGVDEREGFMLALKTLGNKLGGVPAEVIVVDDQF-SPDA 81 Query: 83 AKRLAQELVVRDKVDFLAGFGLTPEALAVAPIAEQAKKPMIIMNAASSIITTKSNYIARF 142 AK+ A L+ R+KVD L+GF + LAVAP A +K ++ NA + + F Sbjct: 82 AKQGADRLIKREKVDILSGFVYSNILLAVAPAAFASKTVVVSANAGPAQLAGAGCNPYFF 141 Query: 143 SMTLPQVSGPMATWAL--KNGIKRVVTLVADYGPGIDAETAFKTNLLGGGGEVVESIRVP 200 S + + A L G +RV + +Y G DA FK L + + Sbjct: 142 SASYQNDAAHEAAGKLMADKGYQRVAIIAPNYPAGKDASAGFKRFL---KKDPAVELFPK 198 Query: 201 LRNPEFAPYIQRIKDAKPQAVFIFVPAGEQSIAFMKGYRERGLAEAGIKVIATGDLTDDH 260 L +FA I +++ A A++ F+P G + F+K Y G+ ++V+ D D Sbjct: 199 LGQLDFATEIAQLRAANIDALYFFLPGG-MGVNFVKQYAAAGMDPKIVRVMPAYDA--DQ 255 Query: 261 VMPAMGDSTLGVITTFHYSAAHDSPENKAFLKSFAAANPDAGR-PNFMAVAAYDGMNAIY 319 M + GD GV T +S+ + +N+AF+ ++ + GR P+ A AYD I Sbjct: 256 QMLSNGDLIAGVANTGQWSSDLPNEQNRAFVAAYL---KEYGRQPSMFASQAYDAAMLID 312 Query: 320 EVSKKLNGKIDGERAM-AILKTMKFVSPRGPIAIDPATRDIVQTVYVRKVEK 370 K + GK++ A+ A +KT F S RG A +Q Y R V K Sbjct: 313 SAVKAVGGKVENREALIAAIKTANFKSVRGGFRF-AANHFPIQNQYARVVTK 363 >gi|300314071|ref|YP_003778163.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 402 Score = 84.3 bits (207), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 91/366 (24%), Positives = 164/366 (44%), Gaps = 23/366 (6%) Query: 27 DTIKVGLIAAFSGPFADYGKQMEGG---IKAYMAQHGDQVAGKKVQVIIKDTTGPSPEIA 83 D IK+G I SG ++D Q GG IK +A G + GKK+++++ D + ++A Sbjct: 29 DVIKIGFITDISGVYSDIDGQ--GGAEAIKMAIADMGGAINGKKIELLVADHQNKA-DVA 85 Query: 84 KRLAQELVVRDKVDFLAGFGLTPEALAVAPIAEQAKKPMIIMNAASSIITTK--SNYIAR 141 A+E + VD L G + ALA A +A + KK + + A S+ +T + S Y Sbjct: 86 ASKAREWFDQQGVDMLIGGTNSGTALASAKVAAEKKKVYMQIGAGSARLTNEECSPYTVH 145 Query: 142 FSMTLPQVSGPMATWALKNGIKRVVTLVADYGPGIDAETAFKTNLLGGGGEVVESIRVPL 201 ++ ++ + +K G K L ADY G E+ + GG VV +++ PL Sbjct: 146 YAYDTVALAKGTGSAVVKQGGKSWFFLTADYAFGHSLESDTANVVKASGGTVVGAVKHPL 205 Query: 202 RNPEFAPYIQRIKDAKPQAVFIFVPAGEQSIAFMKGYRERGLAE----AGIKVIATGDLT 257 +F+ ++ + + +K Q + AG I +K E G+ + AG+ V + Sbjct: 206 GASDFSSFLLQAQSSKAQ-IIGLANAGGDFINSVKAANEFGITKTAKLAGLLVF----IN 260 Query: 258 DDHVMPAMGDSTLGVITTFHYSAAHDSPENKAFLKSFAAANPDAGRPNFMAVAAYDGMNA 317 D H + L + ++++ A + E +AF K + A P+ + A Y Sbjct: 261 DVHSLTLKNTEGLYLTDSWYWDA---NEETRAFAKRYFAVRKK--MPSSLQAADYSAALQ 315 Query: 318 IYEVSKKLNGKIDGERAMAILKTMKFVSPRGPIAIDPATRDIVQTVYVRKVEKIGKEAYN 377 +V K++ G D ++ MA L+ KF A ++ +Y+ +V+ + Y Sbjct: 316 YLKVVKEI-GTDDSDKVMAALRKAKFNDMYQKNGYLRADGRVMHDMYLYQVKAQSESKYP 374 Query: 378 VEFDKF 383 ++ K Sbjct: 375 WDYYKL 380 >gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 82.8 bits (203), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 65/215 (30%), Positives = 106/215 (49%), Gaps = 9/215 (4%) Query: 21 PLAQAE-DTIKVGLIAAFSGPFADYGKQMEGGIKAY---MAQHGDQVAGKKVQVIIKDTT 76 P AQA DTIK+G I SG +AD+ Q GG++A +A G + GKKV+++ D Sbjct: 24 PSAQAAGDTIKIGFITDMSGTYADFDGQ--GGVEAIRMAIADAGGAINGKKVELVFADHQ 81 Query: 77 GPSPEIAKRLAQELVVRDKVDFLAGFGLTPEALAVAPIAEQAKKPMIIMNAASSIITTK- 135 + +IA A+E RD VD L G + +LA+ +A + KK I + A ++ T + Sbjct: 82 NKA-DIAANKAREWFDRDGVDMLVGGVNSAASLAMGKVAGEKKKVFISVGAGTTRQTNEE 140 Query: 136 -SNYIARFSMTLPQVSGPMATWALKNGIKRVVTLVADYGPGIDAETAFKTNLLGGGGEVV 194 + Y +++ ++ + G K L ADY G E + GG VV Sbjct: 141 CNAYTIQYAYDTTALARGTGAAITRQGGKSWYFLTADYAFGTSLEKDTSEVVKSNGGNVV 200 Query: 195 ESIRVPLRNPEFAPYIQRIKDAKPQAVFIFVPAGE 229 + RVPL +F+ ++ + + +K Q + + V G+ Sbjct: 201 GATRVPLATSDFSSFLLQAQSSKAQILGLAVAGGD 235 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 0.134 0.376 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: 1,179,794 Number of extensions: 50327 Number of successful extensions: 193 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 188 Number of HSP's successfully gapped: 17 Length of query: 391 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 304 Effective length of database: 1,207,925 Effective search space: 367209200 Effective search space used: 367209200 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)