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= 0001.3896.p (620 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313294|ref|YP_003777386.1| long chain acyl-CoA synthetase ... 1240 0.0 gi|300311882|ref|YP_003775974.1| long-chain acyl-CoA synthetase ... 98 2e-21 gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligas... 67 3e-12 >gi|300313294|ref|YP_003777386.1| long chain acyl-CoA synthetase [Herbaspirillum seropedicae SmR1] Length = 620 Score = 1240 bits (3209), Expect = 0.0, Method: Compositional matrix adjust. Identities = 595/620 (95%), Positives = 611/620 (98%) Query: 1 MNTPPRYRSFRFGIGGVDVVPGRDGISLVKTRQPLDAYPARLTDKLIHWAKVDPDRTYMA 60 MNTPPRYRSFRFGIGGVDVVPG DG+S+VKTRQPLDAYPARLTDKLIHWA VDPDRTYMA Sbjct: 1 MNTPPRYRSFRFGIGGVDVVPGADGVSIVKTRQPLDAYPARLTDKLIHWATVDPDRTYMA 60 Query: 61 RRDKEGLWRRISYGQALQSARRIGQALLQRGLSAERPLLILSENDLEHAMLVLGCHYAGV 120 RRD++G WRRISYGQALQSARRIGQALLQRGLSAERPLLILSENDLEHAMLVLGCHYAGV Sbjct: 61 RRDQDGQWRRISYGQALQSARRIGQALLQRGLSAERPLLILSENDLEHAMLVLGCHYAGV 120 Query: 121 PYAPVSSAYSLLSKDYAKLRHAVQLLTPGLIFAAHGEKFAAAVNAVAPDIEFVVTEAPPA 180 PYAPVSSAYSLLSKDYAKLRHAVQLLTPGLIFAAHGEKFAAAVNAVAP+IEFVVTEAPPA Sbjct: 121 PYAPVSSAYSLLSKDYAKLRHAVQLLTPGLIFAAHGEKFAAAVNAVAPEIEFVVTEAPPA 180 Query: 181 GRECTLYADLEATRAGDEVERAYAATGPDTIVKFLFTSGSTKMPKAVINTQRMMCSNLQM 240 GRECTLYA+LEATRAGDEVERA+AATGP+TIVKFLFTSGSTKMPKAVINTQRMMCSNLQM Sbjct: 181 GRECTLYAELEATRAGDEVERAFAATGPETIVKFLFTSGSTKMPKAVINTQRMMCSNLQM 240 Query: 241 IVQTFPFLGEEPPILIDWLPWNHTFGANHNVGIVIYNGGTMYIDEGKPTPQGLATTLANL 300 IVQTFPFLGEEPPILIDWLPWNHTFGANHNVGIV+YNGGTMYIDEGKPTPQGLATTLANL Sbjct: 241 IVQTFPFLGEEPPILIDWLPWNHTFGANHNVGIVLYNGGTMYIDEGKPTPQGLATTLANL 300 Query: 301 HEISPTVYFNVPVGWEGIAHALEKDQALREKFYSRLRMQFYAGAALAQPVWDKLHATAEA 360 H+ISPTVYFNVPVGWEGIAHALEKDQALREKFYSRLRMQFYAGAALAQPVWDKLHATAEA Sbjct: 301 HDISPTVYFNVPVGWEGIAHALEKDQALREKFYSRLRMQFYAGAALAQPVWDKLHATAEA 360 Query: 361 TCGERIVMCCGLGMTETSPSALFVADLEVQAGQIGIPTPGMEIKLVPNGDKIEIRYRGPN 420 TCGERIVMCCGLGMTETSPSALFVADLEVQAGQIGIPTPGMEIKLVPNGDKIEIRYRGPN Sbjct: 361 TCGERIVMCCGLGMTETSPSALFVADLEVQAGQIGIPTPGMEIKLVPNGDKIEIRYRGPN 420 Query: 421 VTPGYWRAPEQTAEAFDEEGYFRSGDAVRWLDPQHPDRGFMFDGRVAEDFKLYTGTWVSV 480 VTPGYWRAPEQTAEAFDEEGYFRSGDAVRWLDP HPDRGFMFDGRVAEDFKLYTGTWVSV Sbjct: 421 VTPGYWRAPEQTAEAFDEEGYFRSGDAVRWLDPAHPDRGFMFDGRVAEDFKLYTGTWVSV 480 Query: 481 GPLRALIAHEGAPYLQDAVITGQDRKEIGMLIVPNIERCRQLAGLPADASRAEVFNAAPV 540 GPLRALIAHEGAPYLQDAVITGQDRKEIGMLIVPNIERCRQLA LPA+ASRAEV NAAPV Sbjct: 481 GPLRALIAHEGAPYLQDAVITGQDRKEIGMLIVPNIERCRQLARLPAEASRAEVLNAAPV 540 Query: 541 RDFFQGMLDRLQAHATGSSNRVTRALVLIDPPSFDRGEITDKGSINQRSVLTHRAALVEA 600 RDFFQG+LDRLQ+HATGSSNRVTRALVL+DPPSFDRGEITDKGSINQR+VLTHRAALVE Sbjct: 541 RDFFQGVLDRLQSHATGSSNRVTRALVLVDPPSFDRGEITDKGSINQRAVLTHRAALVET 600 Query: 601 LYAGTDPAVLTAQAALTPAH 620 LYAGTDPAVLT Q AL+PAH Sbjct: 601 LYAGTDPAVLTVQPALSPAH 620 >gi|300311882|ref|YP_003775974.1| long-chain acyl-CoA synthetase [Herbaspirillum seropedicae SmR1] Length = 653 Score = 97.8 bits (242), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 153/665 (23%), Positives = 250/665 (37%), Gaps = 121/665 (18%) Query: 28 LVKTRQPLDAYPARLTDKLIHWAKVDPDRTYMARRDKEGLWRRISYGQALQSARRIGQAL 87 +V+TRQ +A A L+ A+ P+R +D G+W+ S+ Q + R L Sbjct: 1 MVETRQDREA--ATFPRLLLAHARQRPERAAFREKDL-GIWQTTSWRQVAEEVRSFACGL 57 Query: 88 LQRGLSAERPLLILSEN--DLEHAMLVLGCHYAGVPYAPVSSAYSLLSKDYAKLRHAVQL 145 G L I+ N L AM G+P A + A + + + Sbjct: 58 AALGFRRGMSLAIIGNNCPRLYWAMSAAQA-LGGMPVPLYQDAPA------ADMAYVLAD 110 Query: 146 LTPGLIFAAHGEKFAAA--VNAVAPDIEFVVTEAPPAGR---ECTLYADLEATRAGDEVE 200 + A E+ + P I V+ + R + L + G E Sbjct: 111 ANVDFVMAEDQEQVDKVFEIKESLPRIAHVIYDDERGMRNYHQPELLSFARVQELGRAYE 170 Query: 201 RAY--------AATGPDTIVKFLFTSGSTKMPKAVINTQRMMCSNLQMIVQTFPFLGEEP 252 RA+ AA PD + L+TSG+T PK V ++ R M + +V+ F L E Sbjct: 171 RAHPDFFDQEIAAGSPDDVAIILYTSGTTGKPKGVCHSHRAMITTATTLVE-FDHLDEND 229 Query: 253 PILIDWLP------WNHTFGANHNVGIVIYNGGTMYIDEGKPTPQGLATTLANLHEISPT 306 IL +LP + ++F H G + P+ T + +L EI PT Sbjct: 230 DILC-YLPLAWVGDFLYSFAQQHVAGFCL------------NCPESPNTVMTDLREIGPT 276 Query: 307 VYFNVPVGWEGIAHA----LEKDQALREKFY----------------------------- 333 YF P +E I +E L+ K + Sbjct: 277 YYFAPPRVYENILTQVMIRIEDAGWLKRKMFHGFMKVARRVGMRILDGKPGVSLLDRLQY 336 Query: 334 -----------------SRLRMQFYAGAALAQPVWDKLHATAEATCGERIVMCCGLGMTE 376 SRLR+ + G A+ ++D + I + GMTE Sbjct: 337 GLGSLLVYGPLKNVLGMSRLRVAYTGGEAIGPDLFDFYRSLG-------INLKQLYGMTE 389 Query: 377 TSPSALFVADLEVQAGQIGIPTPGMEIKLVPNGDKIEIRYRGPNVTPGYWRAPEQTAEAF 436 T + +V+ +G P G+E+++ NG E+ R P + Y++ P+ TAEA Sbjct: 390 TCVTVCMQPSGDVKLDSVGRPMKGVEVRIDENG---EVLVRSPGLMKEYFKRPDATAEAI 446 Query: 437 DEEGYFRSGDAVRWLDPQHPDRGFMFDGRVAEDFKLYTGTWVSVGPLRALIAHEGAPYLQ 496 D GYF +GDA + H R + K+ +G+ + + + P+++ Sbjct: 447 DANGYFHTGDAGFFDSDGH----LKIIDRAKDVGKMASGSMFAPKYIENKLKF--FPFIK 500 Query: 497 DAVITGQDRKE------IGMLIVPNIERCRQLA--GLPADASRAEVFNAAPVRDFFQGML 548 +AV G R++ I M V N R LA G A+ V+ A +R+ + + Sbjct: 501 EAVTFGNGREQCMAFINIDMDAVGNWAERRNLAYSGYTDLAANPAVY--ALLRECVEKVN 558 Query: 549 DRLQAHATGSSNRVTRALVLIDPPSFDRGEITDKGSINQRSVLTHRAALVEALYAGTDPA 608 L A + +++ R L+L D E+T + + + A L+EALYAG Sbjct: 559 ADLAADPLLADSQIHRFLILHKELDPDDEELTRTRKVRRGFIADKYAVLIEALYAGRASQ 618 Query: 609 VLTAQ 613 + Q Sbjct: 619 YIETQ 623 >gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligase [Herbaspirillum seropedicae SmR1] Length = 566 Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 66/251 (26%), Positives = 102/251 (40%), Gaps = 26/251 (10%) Query: 209 DTIVKFLFTSGSTKMPKAVINTQRMMCSN-LQMIVQTFPFLGEEPPI----LIDWLPWNH 263 D I +T G+T + K + T R + +N LQ P L PI + LP H Sbjct: 205 DDIAFLQYTGGTTGVAKGAVLTHRNLVANVLQAEEWLTPALKAGKPIDQLVFVCALPLYH 264 Query: 264 TFGANHNVGIVIYNGGTMYIDEGKPTPQGLATTLANLHEISPTVYFNVPVGWEGIAHALE 323 F + G + P P+ + + L + + V + +AL Sbjct: 265 IFALTVCNMLGTREGALNLL---IPNPRDIPGFVKELAKYKVNTFPAV----NTLYNALL 317 Query: 324 KDQALREKFYSRLRMQFYAGAALAQPVWDKLHATAEATCGERIVMCCGLGMTETSP-SAL 382 + +S R G A+ + V DK E G G++ETSP ++ Sbjct: 318 NNADFARLDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIE------GYGLSETSPIASA 371 Query: 383 FVADLEVQAGQIGIPTPGMEIKL-------VPNGDKIEIRYRGPNVTPGYWRAPEQTAEA 435 ++ G IG+P P E + VP G EI RGP V PGYW+ P++TA+ Sbjct: 372 NPCTIDEYTGTIGLPLPSTEFAILDDDGQPVPLGQPGEIAIRGPQVMPGYWQRPDETAKV 431 Query: 436 FDEEGYFRSGD 446 +G+F++GD Sbjct: 432 MTPDGFFKTGD 442 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 0.320 0.137 0.417 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: 2,118,538 Number of extensions: 94566 Number of successful extensions: 255 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 258 Number of HSP's successfully gapped: 4 Length of query: 620 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 529 Effective length of database: 1,188,985 Effective search space: 628973065 Effective search space used: 628973065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 133 (55.8 bits)