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= 0003.0141.p (566 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligas... 1073 0.0 gi|300313115|ref|YP_003777207.1| long-chain-fatty-acid-CoA ligas... 171 1e-43 gi|300309365|ref|YP_003773457.1| acetyl-coenzyme A synthetase [H... 155 6e-39 gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA lig... 139 5e-34 gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid li... 134 3e-32 >gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligase [Herbaspirillum seropedicae SmR1] Length = 566 Score = 1073 bits (2776), Expect = 0.0, Method: Compositional matrix adjust. Identities = 522/566 (92%), Positives = 546/566 (96%) Query: 1 MERFWLASYPAGVPADIDPSRYGSLVQMIEEAFAKHADRNAYVCMGKYLRYGELDAMSRA 60 MERFWLASYPAGVPA+IDP RYGSLVQMI+EAF +HADR AYVCMGKYL Y ELD++SRA Sbjct: 1 MERFWLASYPAGVPAEIDPGRYGSLVQMIDEAFVQHADRQAYVCMGKYLSYRELDSLSRA 60 Query: 61 MGAWLQGLGLQKGARVAIMMPNVLQYPIAIAAILRAGYTVVNVNPLYTARELEHQLKDSG 120 +G WLQGLGLQKGARVAIMMPNVLQYPIAIAAILRAGYTVVNVNPLYTARELEHQLKDSG Sbjct: 61 LGGWLQGLGLQKGARVAIMMPNVLQYPIAIAAILRAGYTVVNVNPLYTARELEHQLKDSG 120 Query: 121 AEAIFVLENFACTLQKVVAHTQVKHIVVASMGELLGTLKGAIVNLVVRHVKKMVPSWSLP 180 AEAIFVLENFACTLQKVVAHT +KHIVVASMGELLG LKG +VNLVVRHVKK+VP+WSLP Sbjct: 121 AEAIFVLENFACTLQKVVAHTNIKHIVVASMGELLGALKGTLVNLVVRHVKKLVPAWSLP 180 Query: 181 NAISFSRALSQGEGKTLQKVSLTPDDVAFLQYTGGTTGVAKGAVLTHRNLIANVLQAEEW 240 NAI+FS+ALSQ GKTLQ V+LT DD+AFLQYTGGTTGVAKGAVLTHRNL+ANVLQAEEW Sbjct: 181 NAITFSQALSQARGKTLQPVTLTHDDIAFLQYTGGTTGVAKGAVLTHRNLVANVLQAEEW 240 Query: 241 LTPALKSGKPIDQLVFVCALPLYHIFALTVCNLLGTREGALNLLIPNPRDIPGFVKELAK 300 LTPALK+GKPIDQLVFVCALPLYHIFALTVCN+LGTREGALNLLIPNPRDIPGFVKELAK Sbjct: 241 LTPALKAGKPIDQLVFVCALPLYHIFALTVCNMLGTREGALNLLIPNPRDIPGFVKELAK 300 Query: 301 YKVNTFPAVNTLYNALLNNADFAKLDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIEGY 360 YKVNTFPAVNTLYNALLNNADFA+LDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIEGY Sbjct: 301 YKVNTFPAVNTLYNALLNNADFARLDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIEGY 360 Query: 361 GLSETSPIASANPCTIDEYTGTIGLPLPSTEIAILDDDGHPVPLGQPGEIAIRGPQVMPG 420 GLSETSPIASANPCTIDEYTGTIGLPLPSTE AILDDDG PVPLGQPGEIAIRGPQVMPG Sbjct: 361 GLSETSPIASANPCTIDEYTGTIGLPLPSTEFAILDDDGQPVPLGQPGEIAIRGPQVMPG 420 Query: 421 YWQRPDETAKVMTPDGFFKTGDIGVMDAQGYTKIVDRKKDMILVSGFNVYPNEIEGVVAQ 480 YWQRPDETAKVMTPDGFFKTGDIGVMD +GYTKIVDRKKDMILVSGFNVYPNE+EGVVAQ Sbjct: 421 YWQRPDETAKVMTPDGFFKTGDIGVMDERGYTKIVDRKKDMILVSGFNVYPNEVEGVVAQ 480 Query: 481 HPAVLECACVGVPDEHTGEAVKLFVVRKDKSLTSEQLMAYCKEQFTGYKKPKYIEFRDEL 540 HP VLECACVGVPDEHTGEAVKLFVVRKDK+L++ QLM YCKEQFTGYKKPKYIEFRDEL Sbjct: 481 HPGVLECACVGVPDEHTGEAVKLFVVRKDKTLSAAQLMDYCKEQFTGYKKPKYIEFRDEL 540 Query: 541 PKTNVGKILRRELRDDPAKAPQKQAA 566 PKTNVGKILRRELRD+PAKA QKQAA Sbjct: 541 PKTNVGKILRRELRDEPAKAQQKQAA 566 >gi|300313115|ref|YP_003777207.1| long-chain-fatty-acid-CoA ligase [Herbaspirillum seropedicae SmR1] Length = 556 Score = 171 bits (434), Expect = 1e-43, Method: Compositional matrix adjust. Identities = 139/514 (27%), Positives = 225/514 (43%), Gaps = 43/514 (8%) Query: 51 YGELDAMSRAMGAWLQGLGLQKGARVAIMMPNVLQYPIAIAAILRAGYTVVNVNPLYTAR 110 + E++A A+ L G++KG ++ + N Q + A + G V N T Sbjct: 65 WREINARVDALAHALTRRGVKKGDKMLVHSRNNQQIFESAWAAFKMGVVWVPTNFRITPP 124 Query: 111 ELEHQLKDSGAEAIFVLENFACTLQKVVAHTQVKHIVVASMGELLGTLKGAIVNLVVRHV 170 E + + SGA + FA + V A + VVA G L Sbjct: 125 EAAYLGQSSGACVMLYDRGFAQYVDAVKAASPALEHVVALADARAGEL------------ 172 Query: 171 KKMVPSWSLPNAISFSRALSQGEGKTLQKVSLTPDDVAFLQYTGGTTGVAKGAVLTHRNL 230 + + +G G ++ + DD + YT GTTG K +L+H + Sbjct: 173 -------------DYEALVREGSGAAFREAEVDYDDPLWFFYTSGTTGHPKAGMLSHGQM 219 Query: 231 IANVLQAEEWLTPALKSGKPIDQLVFVCALPLYHIFALTVCNLLGTREGALNLLIPNPRD 290 V L P L Q + PL H V ++ T GA ++L+ + R Sbjct: 220 AFVVTNHLADLMPGLTH-----QSRSLVVAPLSH--GAGVHAVINTARGAASILLSSERL 272 Query: 291 IPGFVKELA-KYKVNTFPAVNTLYNALLNNADFAKLDFSGYRCCVGGGMAVQKSVADKWK 349 + +L KY+V+ V T+ L+ + + D S + + G + ++ Sbjct: 273 VVEEAWQLVEKYRVDNLFTVPTIVKILVEDESVDRYDHSSLKHVIYAGAPMYRADQVYAL 332 Query: 350 KLTGCPIIEGYGLSETSPIASANPCTI--------DEYTGTIGLPLPSTEIAILDDDGHP 401 K G +++ YGL E + + P + GT G+P +IAIL+DDG Sbjct: 333 KKLGKVLVQYYGLGEVTGNITFLPPYLHFEDDAHPQARVGTCGMPRTGMQIAILNDDGQE 392 Query: 402 VPLGQPGEIAIRGPQVMPGYWQRPDETAKVMTPDGFFKTGDIGVMDAQGYTKIVDRKKDM 461 + + GEI +RGP V GY P+ AK D +F TGD+G +D G+ I R DM Sbjct: 393 LAPFETGEICVRGPAVFMGYHNNPEANAKAFKHD-WFHTGDLGHVDQDGFLYITGRSSDM 451 Query: 462 ILVSGFNVYPNEIEGVVAQHPAVLECACVGVPDEHTGEA-VKLFVVRKDKSLTSEQLMAY 520 + G NVYP EIE + HPAV E A +GVPD GE+ + + V + + + E L+A+ Sbjct: 452 YISGGSNVYPREIEEALLTHPAVSEVAVLGVPDPKWGESGLAVIVCKAGQQVDGEALLAH 511 Query: 521 CKEQFTGYKKPKYIEFRDELPKTNVGKILRRELR 554 + + YK P+ + D +PK+ GKI++++++ Sbjct: 512 LESRIGKYKWPRRFIYWDSMPKSGYGKIVKKQIK 545 >gi|300309365|ref|YP_003773457.1| acetyl-coenzyme A synthetase [Herbaspirillum seropedicae SmR1] Length = 549 Score = 155 bits (393), Expect = 6e-39, Method: Compositional matrix adjust. Identities = 155/575 (26%), Positives = 241/575 (41%), Gaps = 68/575 (11%) Query: 7 ASYPAGVPADID---PSRYGSLVQMIEEAFAKHADRNAYVCMG-----KYLRYGELDAMS 58 A Y AG P+ + P+ + ++ Q + +A + R A +C Y +L +S Sbjct: 14 AHYRAGNPSPYEWQIPTHF-NIAQAACDRWADGSGRTAIICEDADGSVTSYSYDQLKILS 72 Query: 59 RAMGAWLQGLGLQKGARVAIMMPNVLQYPIAIAAILRAGYTVVNVNPLYTARELEHQLKD 118 L+ G+ +G R+ I + ++ I A + G V + L+ + ++L + Sbjct: 73 DRFANALRAAGVGRGDRIGIYLSQRIETVITHLAAYKLGAITVPLFYLFGPDAIAYRLDN 132 Query: 119 SGAEAIFVLENFACTLQKVVAHTQVKHIVVASMGELLGTLKGAIVNLVVRHVKKMVPSWS 178 SGA A+ V + G TL G + L + + Sbjct: 133 SGAVAL----------------------VTDASGMEKATLAGELPALRLVFCVES-SDLV 169 Query: 179 LPNAISFSRALSQGEGKTLQKVSLTPDDVAFLQYTGGTTGVAKGAVLTHRNLIANV---- 234 LP F L + L V DD A + YT GTTG AKGA+ HR L+ ++ Sbjct: 170 LPQTTDFWDRLHAAPAE-LDPVLTLADDPAMIIYTSGTTGKAKGALHAHRVLLGHLPGVE 228 Query: 235 -------LQAEEWLTPALKSGKPIDQLVFVCALPLYHIFALTVCNLLGTREGALNLLIPN 287 + + + TPA I L+ V LYH A+ L Sbjct: 229 VSHDSFPQEGDRFWTPA--DWAWIGGLLDVLLPSLYHGVAVVARRL-------------E 273 Query: 288 PRDIPGFVKELAKYKVNTFPAVNTLYNALLNNADF-AKLDFSGYRCCVGGGMAVQKSVAD 346 D LA++++ T L A A+ DFS R GG + + Sbjct: 274 KFDAAEVFGLLARHQIRNVFFPPTALKMLRGAATVRAQADFS-LRSVASGGETLGDDLIA 332 Query: 347 KWKKLTGCPIIEGYGLSETSPIASANPCTIDEYTGTIGLPLPSTEIAILDDDGHPVPLGQ 406 ++ G I E YG +E + + S++ +G++G +P + I+D+ G +P G Sbjct: 333 WGREALGVTINEFYGQTECNLVVSSSSHCYPSVSGSMGRAVPGHVVQIVDEQGQVLPHGT 392 Query: 407 PGEIAIRGPQ--VMPGYWQRPDETAKVMTPDGFFKTGDIGVMDAQGYTKIVDRKKDMILV 464 G IAIR P + YW+ + T + D F TGD+G MD QGY + + R D+I Sbjct: 393 VGNIAIRAPDPVMFLRYWRNEEATREKFAGD-FLLTGDLGSMDEQGYIRYLGRNDDVITS 451 Query: 465 SGFNVYPNEIEGVVAQHPAVLECACVGVPDEHTGEAVKLFVVRKDKSLTSEQLMA----Y 520 +G+ + P IE + +HPAV A VGV D E VK FVV KD E L A + Sbjct: 452 AGYRIGPAAIEECLMRHPAVRIAAVVGVKDALRTEVVKAFVVLKDGVTPDEALKAELQQH 511 Query: 521 CKEQFTGYKKPKYIEFRDELPKTNVGKILRRELRD 555 + Q ++ P+ I F LP T GKI+R+ L++ Sbjct: 512 VRAQLAAHEYPRLISFVAALPTTATGKIMRKTLKE 546 >gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA ligase [Herbaspirillum seropedicae SmR1] Length = 545 Score = 139 bits (351), Expect = 5e-34, Method: Compositional matrix adjust. Identities = 149/562 (26%), Positives = 247/562 (43%), Gaps = 55/562 (9%) Query: 19 PSRYGS---LVQMIEEAFAKHADRNAYVCMGKYLRYGELDAMSRAMGAWLQGLGLQKGAR 75 PS YG + Q++ A A A + + L Y + + L+ +GLQ G Sbjct: 9 PSAYGYPLLIKQLLHSALAT-ASGQEIIYGQRRLSYAGFYERVQRLANALKEMGLQPGNT 67 Query: 76 VAIMMPNVLQYPIAIAAILRAGYTVVNVNPLYTARELEHQLKDSGAEAIFVLENFACTLQ 135 VA+M + +Y A+ G + VN + ++ + L + A+ + V +F L+ Sbjct: 68 VAVMDWDSNRYLECFFAVPMMGCVLQTVNVRLSPEQIAYTLNHAQADVLLVNSDFLPLLK 127 Query: 136 KVVAHTQVKHIVVASMGELLGTLKGAIVNLVVRHVKKMVPSWSLPN-AISFSRALSQGEG 194 ++ GEL + V P P A + L+Q E Sbjct: 128 QI-------------RGEL------TTLTRCVWLTDDATPCPRGPGFAGEYEELLAQAE- 167 Query: 195 KTLQKVSLTPDDVAFLQYTGGTTGVAKGAVLTHRNLIANVLQAEEWLTPALKSGKPIDQL 254 + A YT GTTG+ KG +HR L+ + L L A + G+ Sbjct: 168 PACDFPDFDENARATTFYTTGTTGLPKGVYFSHRQLVLHTLATTAGLALAPQQGRFHRDD 227 Query: 255 VFVCALPLYHIFAL---TVCNLLGTREGALNLLIPNPRDIPGFVKELAKYKVNTFP-AVN 310 V++ P++H+ A V + G ++ + P R +P + L + + TF V Sbjct: 228 VYMPLTPMFHVHAWGLPYVATMAGVKQ-----VYPG-RYVPDTICRLIREEKVTFSHCVP 281 Query: 311 TLYNALLNNADFAKLDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIEGYGLSETSPIAS 370 T+ +L + + D SG++ +GG A+ S+A K + G + GYG+SET P+ + Sbjct: 282 TILQMVLTSEQAREADLSGWKMIIGGS-AMTGSLA-KMARDRGIDVFTGYGMSETCPVLT 339 Query: 371 ANPCTIDEYTG--------TIGLPLPSTEIAILDDDGHPVPL--GQPGEIAIRGPQVMPG 420 +E G G PLP ++ +D + P GE+ +R P + G Sbjct: 340 LAQVPTEELGGEREAAIRVKTGRPLPLVDLRTVDGEMQDCPRDGSTTGEVVVRAPWLTQG 399 Query: 421 YWQRPDETAKVMTPDGFFKTGDIGVMDAQGYTKIVDRKKDMILVSGFNVYPNEIEGVVAQ 480 Y + E ++ + G+ T DIG +DA+GY ++ DR KD+I G V +IE ++A+ Sbjct: 400 YLHQA-EASEELWRGGWLHTQDIGHLDAEGYLQVTDRIKDVIKTGGEWVSSLQIEDIIAR 458 Query: 481 HPAVLECACVGVPDEHTGEA-VKLFVVRKDKSLTSEQLM------AYCKEQFTGYKKPKY 533 HPAV E A +G+ D GE V L V++KD + SE + A + Y P Sbjct: 459 HPAVAETAVIGIQDGKWGERPVALVVLKKDAAAVSEDDIREHVRAAAEAGAISRYGVPDR 518 Query: 534 IEFRDELPKTNVGKILRRELRD 555 + F EL +T+VGK+ +R +R+ Sbjct: 519 VRFVAELARTSVGKLNKRVMRE 540 >gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid ligase II protein [Herbaspirillum seropedicae SmR1] Length = 546 Score = 134 bits (336), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 150/564 (26%), Positives = 243/564 (43%), Gaps = 66/564 (11%) Query: 18 DPSRYGSL--VQMIEEAFAKHADRNAYVCMGKYLRYGELDAMSRAMGAWLQGLGLQKGAR 75 + + Y +L + I A A + R A + + + +R + + LQGLG+ K Sbjct: 11 NAANYAALTPIDFIARAAAVYGKRTAIIHGALRQDWDQTYRRTRRLASALQGLGVGKNDT 70 Query: 76 VAIMMPNVLQYPIAIAAILRAGYTVVNVNPLYTARELEHQLKDSGAEAIFVLENFACTLQ 135 V+ M+PN A + AG + +N A + L+ A+ + + FA Q Sbjct: 71 VSAMLPNTPAMVEAHFGVPMAGAVLNALNIRLDAESIVFMLRHGEAKVLLIDSEFAALAQ 130 Query: 136 KVVAHTQVKHIVVASMGELLGTLKGAIVNLVVRHVKKMVPSWSLPNAISFSRALSQGEGK 195 ++ TQ+ + + + + LG A + + L+ G+ Sbjct: 131 QL--RTQLPALKIVEVFDELGPPPVAGERF---------------GHLEYEALLAGGDEH 173 Query: 196 TLQKVSLTPDDVAFLQYTGGTTGVAKGAVLTHR----NLIANVLQAEEWLTPALKSGKPI 251 ++ D L YT GTTG KG V HR N ++N+L EW P Sbjct: 174 FDWQMPADEWDAIALNYTSGTTGDPKGVVYHHRGAALNAVSNIL---EWDLP-------- 222 Query: 252 DQLVFVCALPLYHIFALTVCNLLGTREGALNLLIPNPRDIPGFVKEL-AKYKVNTFPAVN 310 V++ LP++H + R G +N+ + P V +L A++ + + A Sbjct: 223 KHPVYLWTLPMFHCNGWCFPWTVAARAG-VNVCLRKFE--PKLVFDLIAEHGITHYCAAP 279 Query: 311 TLYNALLNNADFAKLDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIEGYGLSETSPIAS 370 ++ AL N + + G + G +V K + + + YGL+E A+ Sbjct: 280 IVHAALANAPEGWRAGIRGPVKAMVAGAPPPAAVLAKMEAMQ-FELTHVYGLTEVYGPAA 338 Query: 371 A-------NPCTIDE-----------YTGTIGLPLPSTE-IAILDDDGHPVPLGQPGEIA 411 N ++D+ Y G+ + S + +A + DG + GEI Sbjct: 339 VCAEQDEWNTLSVDQRAVQKSRQGVRYHLQSGVTVLSPDTMAPVAADGEEI-----GEIM 393 Query: 412 IRGPQVMPGYWQRPDETAKVMTPDGFFKTGDIGVMDAQGYTKIVDRKKDMILVSGFNVYP 471 RG M GY + T + G+F TGD+GVM+A GY KI DR KD+I+ G N+ Sbjct: 394 FRGNICMKGYLKNDRATHEAFA-GGWFHTGDLGVMNADGYIKIKDRSKDIIISGGENISS 452 Query: 472 NEIEGVVAQHPAVLECACVGVPDEHTGEAVKLFV-VRKDKSLTSEQLMAYCKEQFTGYKK 530 E+E V+ +HPAVL A V PDE GE FV +++ + + +L +C+ G+K Sbjct: 453 VEVEDVLYRHPAVLAAAVVAQPDEKWGETPCAFVELKEGAEVGAAELTEFCRSHLAGFKV 512 Query: 531 PKYIEFRDELPKTNVGKILRRELR 554 PK I F LPKT+ GKI + ELR Sbjct: 513 PKAIYF-GPLPKTSTGKIQKFELR 535 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 0.411 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: 1,820,088 Number of extensions: 77837 Number of successful extensions: 241 Number of sequences better than 1.0e-08: 13 Number of HSP's gapped: 208 Number of HSP's successfully gapped: 18 Length of query: 566 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 476 Effective length of database: 1,193,720 Effective search space: 568210720 Effective search space used: 568210720 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)