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= 0001.3002.p (404 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312339|ref|YP_003776431.1| branched-chain amino acid ABC t... 786 0.0 gi|300314071|ref|YP_003778163.1| amino acid ABC transporter peri... 541 e-155 gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC t... 510 e-146 gi|300312372|ref|YP_003776464.1| branched-chain amino acid ABC t... 359 e-100 gi|300313931|ref|YP_003778023.1| branched-chain amino acid ABC t... 105 5e-24 >gi|300312339|ref|YP_003776431.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 786 bits (2030), Expect = 0.0, Method: Compositional matrix adjust. Identities = 378/404 (93%), Positives = 394/404 (97%) Query: 1 MTTSTTLGRLAAACAMAGIFSGPALAQASHDAVRIGFITDMSGPYADTDGLGGLEAIRMA 60 M+TST L RLAAACA+AGIFSG ALAQ S+DAVRIGFITDMSGPYADTDGLGGLEAIRMA Sbjct: 1 MSTSTPLRRLAAACAIAGIFSGAALAQVSNDAVRIGFITDMSGPYADTDGLGGLEAIRMA 60 Query: 61 VADYGGKVLGKPIEVLSADHQNKADIAATRAREWVDERGLDMLIGGVNSATALSMNKVMA 120 VAD+GG VLGKPIEV+SADHQNKADIAATRAREW DERGLDMLIGGVNSATALSMNKVMA Sbjct: 61 VADFGGTVLGKPIEVISADHQNKADIAATRAREWADERGLDMLIGGVNSATALSMNKVMA 120 Query: 121 EKKRVYINIGAGTARLTNEECTPYTVHYEYDTVALAKGTASAVIKQGGKSWFFLVADYAF 180 EKKRVYINIGAGTARLTNEECTPYTVHYEYDTVALAKGTASAVIKQGGKSWFFLVADYAF Sbjct: 121 EKKRVYINIGAGTARLTNEECTPYTVHYEYDTVALAKGTASAVIKQGGKSWFFLVADYAF 180 Query: 181 GHSLANDTAAVVKASGGTVVGSIKHPPQSSDLSSFLLQAQASKAQILGLANAGEDTVNAI 240 GHSLANDT+AVVKASGGTVVGSIKHPPQSSDLSSFLLQAQASKAQILGLANAGEDTVN+I Sbjct: 181 GHSLANDTSAVVKASGGTVVGSIKHPPQSSDLSSFLLQAQASKAQILGLANAGEDTVNSI 240 Query: 241 KAAKEFGVTKTMKLVGLLMVINDIHALGLANAQGLMMTDSWYWDKDDASRKFAQRFYQKM 300 KAAKEFGVTKTMKLVGLLMVINDIHALGLANA+GLMMTDSWYWDKD+ SRKFA+RF+QKM Sbjct: 241 KAAKEFGVTKTMKLVGLLMVINDIHALGLANAEGLMMTDSWYWDKDEPSRKFAERFFQKM 300 Query: 301 KKMPSTHQAAAYSATMTYLKAVEAIGTDDATKVMAQLKKTRIDDFYNKGYIRADGRNIHD 360 KKMPSTHQAAAYSAT TYLKAV+AIGTDD+TKVMAQLKKTRIDDFYNKG IRADGRNIHD Sbjct: 301 KKMPSTHQAAAYSATTTYLKAVQAIGTDDSTKVMAQLKKTRIDDFYNKGSIRADGRNIHD 360 Query: 361 MYLYQVKSPAQSKQPWDYLTLLDTIPGEQAFTSVADSKCSLLKQ 404 MYLYQVKSPA+SK+PWDYL LL+TIPGEQAFTSVADSKCSLLKQ Sbjct: 361 MYLYQVKSPAESKKPWDYLKLLETIPGEQAFTSVADSKCSLLKQ 404 >gi|300314071|ref|YP_003778163.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 402 Score = 541 bits (1394), Expect = e-155, Method: Compositional matrix adjust. Identities = 254/378 (67%), Positives = 312/378 (82%), Gaps = 1/378 (0%) Query: 27 QASHDAVRIGFITDMSGPYADTDGLGGLEAIRMAVADYGGKVLGKPIEVLSADHQNKADI 86 Q S D ++IGFITD+SG Y+D DG GG EAI+MA+AD GG + GK IE+L ADHQNKAD+ Sbjct: 25 QISGDVIKIGFITDISGVYSDIDGQGGAEAIKMAIADMGGAINGKKIELLVADHQNKADV 84 Query: 87 AATRAREWVDERGLDMLIGGVNSATALSMNKVMAEKKRVYINIGAGTARLTNEECTPYTV 146 AA++AREW D++G+DMLIGG NS TAL+ KV AEKK+VY+ IGAG+ARLTNEEC+PYTV Sbjct: 85 AASKAREWFDQQGVDMLIGGTNSGTALASAKVAAEKKKVYMQIGAGSARLTNEECSPYTV 144 Query: 147 HYEYDTVALAKGTASAVIKQGGKSWFFLVADYAFGHSLANDTAAVVKASGGTVVGSIKHP 206 HY YDTVALAKGT SAV+KQGGKSWFFL ADYAFGHSL +DTA VVKASGGTVVG++KHP Sbjct: 145 HYAYDTVALAKGTGSAVVKQGGKSWFFLTADYAFGHSLESDTANVVKASGGTVVGAVKHP 204 Query: 207 PQSSDLSSFLLQAQASKAQILGLANAGEDTVNAIKAAKEFGVTKTMKLVGLLMVINDIHA 266 +SD SSFLLQAQ+SKAQI+GLANAG D +N++KAA EFG+TKT KL GLL+ IND+H+ Sbjct: 205 LGASDFSSFLLQAQSSKAQIIGLANAGGDFINSVKAANEFGITKTAKLAGLLVFINDVHS 264 Query: 267 LGLANAQGLMMTDSWYWDKDDASRKFAQRFYQKMKKMPSTHQAAAYSATMTYLKAVEAIG 326 L L N +GL +TDSWYWD ++ +R FA+R++ KKMPS+ QAA YSA + YLK V+ IG Sbjct: 265 LTLKNTEGLYLTDSWYWDANEETRAFAKRYFAVRKKMPSSLQAADYSAALQYLKVVKEIG 324 Query: 327 TDDATKVMAQLKKTRIDDFYNK-GYIRADGRNIHDMYLYQVKSPAQSKQPWDYLTLLDTI 385 TDD+ KVMA L+K + +D Y K GY+RADGR +HDMYLYQVK+ ++SK PWDY L+ TI Sbjct: 325 TDDSDKVMAALRKAKFNDMYQKNGYLRADGRVMHDMYLYQVKAQSESKYPWDYYKLVQTI 384 Query: 386 PGEQAFTSVADSKCSLLK 403 P EQA+T+ A+SKC+ K Sbjct: 385 PAEQAWTTKAESKCAAWK 402 >gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 510 bits (1314), Expect = e-146, Method: Compositional matrix adjust. Identities = 244/394 (61%), Positives = 306/394 (77%), Gaps = 2/394 (0%) Query: 11 AAACAMAGIFSGPALAQASHDAVRIGFITDMSGPYADTDGLGGLEAIRMAVADYGGKVLG 70 A ACA+ G P+ AQA+ D ++IGFITDMSG YAD DG GG+EAIRMA+AD GG + G Sbjct: 12 ATACALLGAAILPS-AQAAGDTIKIGFITDMSGTYADFDGQGGVEAIRMAIADAGGAING 70 Query: 71 KPIEVLSADHQNKADIAATRAREWVDERGLDMLIGGVNSATALSMNKVMAEKKRVYINIG 130 K +E++ ADHQNKADIAA +AREW D G+DML+GGVNSA +L+M KV EKK+V+I++G Sbjct: 71 KKVELVFADHQNKADIAANKAREWFDRDGVDMLVGGVNSAASLAMGKVAGEKKKVFISVG 130 Query: 131 AGTARLTNEECTPYTVHYEYDTVALAKGTASAVIKQGGKSWFFLVADYAFGHSLANDTAA 190 AGT R TNEEC YT+ Y YDT ALA+GT +A+ +QGGKSW+FL ADYAFG SL DT+ Sbjct: 131 AGTTRQTNEECNAYTIQYAYDTTALARGTGAAITRQGGKSWYFLTADYAFGTSLEKDTSE 190 Query: 191 VVKASGGTVVGSIKHPPQSSDLSSFLLQAQASKAQILGLANAGEDTVNAIKAAKEFGVTK 250 VVK++GG VVG+ + P +SD SSFLLQAQ+SKAQILGLA AG D +NAIKAA EFGV K Sbjct: 191 VVKSNGGNVVGATRVPLATSDFSSFLLQAQSSKAQILGLAVAGGDVINAIKAANEFGVNK 250 Query: 251 TMKLVGLLMVINDIHALGLANAQGLMMTDSWYWDKDDASRKFAQRFYQKMKKMPSTHQAA 310 TMKL GLL+ IND H+LGL+ QG+ +TD WYWD +D +R +A R++ KMKKMPS QA Sbjct: 251 TMKLAGLLIFINDTHSLGLSLTQGMYLTDGWYWDLNDQTRAWANRYFMKMKKMPSMFQAG 310 Query: 311 AYSATMTYLKAVEAIGTDDATKVMAQLKKTRIDDFY-NKGYIRADGRNIHDMYLYQVKSP 369 SA YLKAV+A+G+ DA KVM L+K RI+DF+ + G +R DGR +HDMYL +VK P Sbjct: 311 DASAVGQYLKAVKAVGSTDADKVMDYLRKNRINDFFTSNGVVRPDGRMVHDMYLMEVKKP 370 Query: 370 AQSKQPWDYLTLLDTIPGEQAFTSVADSKCSLLK 403 ++SK+PWDY L+ TIPGEQA+ + A+SKC+L K Sbjct: 371 SESKRPWDYYKLVQTIPGEQAYMTKAESKCALWK 404 >gi|300312372|ref|YP_003776464.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 410 Score = 359 bits (921), Expect = e-100, Method: Compositional matrix adjust. Identities = 198/407 (48%), Positives = 264/407 (64%), Gaps = 11/407 (2%) Query: 7 LGRLAAACAMAGIFSG-----PALAQASHDAVRIGFITDMSGPYADTDGLGGLEAIRMAV 61 LGR A A+A S PA AQ + + V+IG +TDMSGPY+ G G + A +MAV Sbjct: 6 LGRSLTAAAVACTVSLAATAIPAWAQDA-NTVKIGVLTDMSGPYSAMGGQGSVVAAKMAV 64 Query: 62 AD-YGGKVLGKPIEVLSADHQNKADIAATRAREWVDERGLDMLIGGVNSATALSMNKVMA 120 D + G IE+LSAD+QNK D+ TRAREW+D ++ + NS+ AL++ K++ Sbjct: 65 EDCLKNECKGMKIEILSADNQNKPDVGVTRAREWLDRDKVEAIADLTNSSVALAVQKLIK 124 Query: 121 EKKRVYINIGAGTARLTNEECTPYTVHYEYDTVALAKGTASAVIKQGGKSWFFLVADYAF 180 +K + + G T LT EC P H+ +DT + A G A+A+ K G KSW+F+ DYAF Sbjct: 125 DKGGIAMYSGPATGALTTAECAPNGFHWMFDTYSQAAGAAAALTKLGNKSWYFVTVDYAF 184 Query: 181 GHSLANDTAAVVKASGGTVVGSIKHPPQSSDLSSFLLQAQASKAQILGLANAGEDTVNAI 240 GHSL D + VVKA+GGTVVGS++HP +SD SSFLLQAQASKAQ++GLA+ G D VNAI Sbjct: 185 GHSLEKDASDVVKANGGTVVGSVRHPLNASDFSSFLLQAQASKAQVIGLADGGTDVVNAI 244 Query: 241 KAAKEFGV-TKTMKLVGLLMVINDIHALGLANAQGLMMTDSWYWDKDDASRKFAQRFYQK 299 K A+ F V K +LV LL+ ++D+HALGL AQGL+ TD +YWD D+ +R F++RF + Sbjct: 245 KQARSFAVGGKDQRLVALLVFLSDVHALGLEAAQGLVYTDGFYWDYDEQTRAFSKRFESQ 304 Query: 300 MKKM-PSTHQAAAYSATMTYLKAVEAIGTDDATKVMAQLKKTRI-DDFYNKGYIRADGRN 357 K + P+ QA YS+ +LKA A T D V ++++ I D IR DGR Sbjct: 305 FKNIKPTMVQAGVYSSVYQFLKARAAAKTSDWKVVAQKMREIPIADAVMRNASIRPDGRV 364 Query: 358 IHDMYLYQVKSPAQSKQPWDYLTLLDTIPGEQAFTSVADSKCSLLKQ 404 IHDMYLYQVK+PA+SK PWDYL LL IP +QAF + D+ C L+KQ Sbjct: 365 IHDMYLYQVKTPAESKGPWDYLKLLSVIPAQQAFRPM-DAACPLVKQ 410 >gi|300313931|ref|YP_003778023.1| branched-chain amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 397 Score = 105 bits (263), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 100/407 (24%), Positives = 174/407 (42%), Gaps = 16/407 (3%) Query: 1 MTTSTTLGRLAAACAMAGIFSGPALAQASHDAVRIGFITDMSGPYADTDGLGGLEAIRMA 60 M + +L+A A + AQA +++ G MSGP+A L +++A Sbjct: 1 MISRRHFLKLSALAAPGALSYHDVFAQA--ESIAFGCPVPMSGPFAANGKFADL-GMKLA 57 Query: 61 VADYGGKVLGKPIEVLSADHQNKADIAATRAREWVDERGLDMLIGGVNSATALSMNKVMA 120 + YG KVLGK ++ D + K A + +E + E+G GG+ S AL+M K Sbjct: 58 LQKYG-KVLGKSTSYVNLDTEGKPATAVRKMQESI-EKGTRFFAGGILSGEALAMGKEAD 115 Query: 121 EKKRVYINIGAGTARLTNEECTPYTVHYEYDTVALAKGTASAVIKQ--GGKSWFFLVADY 178 + V+I AG +T +C T + T + T ++++ K W+ + Y Sbjct: 116 KAGAVFITT-AGADEITGSDCNRATFRWSVPTFGAIEQTVRPLLEKMPNAKRWYTITPQY 174 Query: 179 AFGHSLANDTAAVVKASGGTVVGSIKHPPQSSDLSSFLLQAQASKAQILGLANAGEDTVN 238 FG L + + K G VG+ H + S +L A A+K +L L N G + + Sbjct: 175 VFGEGLLSAAKNIFKEKGIEHVGNSYHSLTEKEFSGYLTNAIAAKPDVLLLLNFGSQSSD 234 Query: 239 AIKAAKEFGVTKTMK-LVGLLMVINDIHALGLANAQGLMMTDSWYWDKDDA--SRKFAQR 295 ++ A FG+ L+ + LG G+ + YW DA +++F + Sbjct: 235 TLRQAVSFGMKNNCTILMAWASGLEQFETLGADICDGVYF-GAQYWHAIDAPFNKEFVKL 293 Query: 296 FYQKMKKMPSTHQAAAYSATMTYLKAVEAIGTDDATKVMAQLKKTRIDDFYNKGYIR-AD 354 +K P+ A +Y T L A+ + D V+A ++ + + IR D Sbjct: 294 VNDNLKIDPNYSLAGSYICTKIILDAIIKANSTDPKAVIAAMEGMKYEGLTGSEEIRKGD 353 Query: 355 GRNIHDMYLYQVKSPAQSKQPWDYLTLLDTIPGEQAFTSVADSKCSL 401 + I + YL + K+ A+ DY D + ++F + ++C L Sbjct: 354 HQVIKNYYLLKGKAKAKMANKNDY---ADIVSSGKSFLPLEKTQCKL 397 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 0.317 0.130 0.373 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: 1,197,365 Number of extensions: 48401 Number of successful extensions: 216 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 204 Number of HSP's successfully gapped: 12 Length of query: 404 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 317 Effective length of database: 1,207,925 Effective search space: 382912225 Effective search space used: 382912225 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: 132 (55.5 bits)