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= 0004.0125.p (479 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid li... 525 e-150 gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA lig... 186 3e-48 gi|300313115|ref|YP_003777207.1| long-chain-fatty-acid-CoA ligas... 173 2e-44 gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligas... 108 7e-25 gi|300309365|ref|YP_003773457.1| acetyl-coenzyme A synthetase [H... 101 1e-22 >gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid ligase II protein [Herbaspirillum seropedicae SmR1] Length = 546 Score = 525 bits (1352), Expect = e-150, Method: Compositional matrix adjust. Identities = 256/476 (53%), Positives = 339/476 (71%), Gaps = 3/476 (0%) Query: 1 VSILAPNTPAMLESHFGIPLSGAVLNSINCRLDSDGVRFILQHGECKILLVDREFSELVS 60 VS + PNTPAM+E+HFG+P++GAVLN++N RLD++ + F+L+HGE K+LL+D EF+ L Sbjct: 71 VSAMLPNTPAMVEAHFGVPMAGAVLNALNIRLDAESIVFMLRHGEAKVLLIDSEFAALAQ 130 Query: 61 RAIADMPDKPLIVDINDVEAPP--GKAIGELDYESLLQEGAPDFEGIWPSDEWDAIALNY 118 + +P ++ +++ PP G+ G L+YE+LL G F+ P+DEWDAIALNY Sbjct: 131 QLRTQLPALKIVEVFDELGPPPVAGERFGHLEYEALLAGGDEHFDWQMPADEWDAIALNY 190 Query: 119 TSGTTSDPKGVVPSHRGTYVMSMLQLTDWGMPRNPVYLWTLPMFHANGWCFTWAITAAAG 178 TSGTT DPKGVV HRG + ++ + +W +P++PVYLWTLPMFH NGWCF W + A AG Sbjct: 191 TSGTTGDPKGVVYHHRGAALNAVSNILEWDLPKHPVYLWTLPMFHCNGWCFPWTVAARAG 250 Query: 179 THVCMRKVTARNIFDAIADHGVNHFCAAPIVLSSIASAPESEKRPLPHSVRVRTAGSPPP 238 +VC+RK + +FD IA+HG+ H+CAAPIV +++A+APE + + V+ AG+PPP Sbjct: 251 VNVCLRKFEPKLVFDLIAEHGITHYCAAPIVHAALANAPEGWRAGIRGPVKAMVAGAPPP 310 Query: 239 AAVLKAVLALGFEVEHVYGITEASGTPVSCYINPAWSQYDKDEQSRLMARQGNRSAALEG 298 AAVL + A+ FE+ HVYG+TE G C W+ D+++ +RQG R G Sbjct: 311 AAVLAKMEAMQFELTHVYGLTEVYGPAAVCAEQDEWNTLSVDQRAVQKSRQGVRYHLQSG 370 Query: 299 LMVADPDTLEPVPFDGKTQGELLLKGNIVMKGYLKNEEATENAFAGGWFHTGDVAVVHAD 358 + V PDT+ PV DG+ GE++ +GNI MKGYLKN+ AT AFAGGWFHTGD+ V++AD Sbjct: 371 VTVLSPDTMAPVAADGEEIGEIMFRGNICMKGYLKNDRATHEAFAGGWFHTGDLGVMNAD 430 Query: 359 GYVQITDRSKDVIISGGENISSVEVEDVLHCHPAVLIAAVVSQPDAKWGETPCAFIELKA 418 GY++I DRSKD+IISGGENISSVEVEDVL+ HPAVL AAVV+QPD KWGETPCAF+ELK Sbjct: 431 GYIKIKDRSKDIIISGGENISSVEVEDVLYRHPAVLAAAVVAQPDEKWGETPCAFVELKE 490 Query: 419 GIEQPDESEIIAFCRERLAHFKCPKQVIFCELPKTGTGKIQKFRLRELVGSRTAIT 474 G E +E+ FCR LA FK PK + F LPKT TGKIQKF LR+ + S +AI Sbjct: 491 GAEV-GAAELTEFCRSHLAGFKVPKAIYFGPLPKTSTGKIQKFELRKRMKSDSAIN 545 >gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA ligase [Herbaspirillum seropedicae SmR1] Length = 545 Score = 186 bits (473), Expect = 3e-48, Method: Compositional matrix adjust. Identities = 145/484 (29%), Positives = 233/484 (48%), Gaps = 30/484 (6%) Query: 1 VSILAPNTPAMLESHFGIPLSGAVLNSINCRLDSDGVRFILQHGECKILLVDREFSELVS 60 V+++ ++ LE F +P+ G VL ++N RL + + + L H + +LLV+ +F L+ Sbjct: 68 VAVMDWDSNRYLECFFAVPMMGCVLQTVNVRLSPEQIAYTLNHAQADVLLVNSDFLPLLK 127 Query: 61 RAIADMPDKPLIVDINDVEAP----PGKAIGELDYESLLQEGAP--DFEGIWPSDEWDAI 114 + ++ V + D P PG A GE YE LL + P DF DE Sbjct: 128 QIRGELTTLTRCVWLTDDATPCPRGPGFA-GE--YEELLAQAEPACDFPDF---DENARA 181 Query: 115 ALNYTSGTTSDPKGVVPSHRGTYVMSMLQLTDWGMP-------RNPVYLWTLPMFHANGW 167 YT+GTT PKGV SHR + ++ + R+ VY+ PMFH + W Sbjct: 182 TTFYTTGTTGLPKGVYFSHRQLVLHTLATTAGLALAPQQGRFHRDDVYMPLTPMFHVHAW 241 Query: 168 CFTWAITAAAGTHVCMRKVTARNIFDAIADHGVNHFCAAPIVLSSIASAPESEKRPLPHS 227 + T A V + I I + V P +L + ++ ++ + L Sbjct: 242 GLPYVATMAGVKQVYPGRYVPDTICRLIREEKVTFSHCVPTILQMVLTSEQAREADL-SG 300 Query: 228 VRVRTAGSPPPAAVLKAVLALGFEVEHVYGITEASGTPVSCYINPAWSQYDKDEQSRLMA 287 ++ GS ++ K G +V YG++E PV + + ++ + Sbjct: 301 WKMIIGGSAMTGSLAKMARDRGIDVFTGYGMSETC--PVLTLAQVPTEELGGEREAAIRV 358 Query: 288 RQGNRSAALEGLMVADPDTLEPVPFDGKTQGELLLKGNIVMKGYLKNEEATENAFAGGWF 347 + G R L L D + ++ P DG T GE++++ + +GYL EA+E + GGW Sbjct: 359 KTG-RPLPLVDLRTVDGE-MQDCPRDGSTTGEVVVRAPWLTQGYLHQAEASEELWRGGWL 416 Query: 348 HTGDVAVVHADGYVQITDRSKDVIISGGENISSVEVEDVLHCHPAVLIAAVVSQPDAKWG 407 HT D+ + A+GY+Q+TDR KDVI +GGE +SS+++ED++ HPAV AV+ D KWG Sbjct: 417 HTQDIGHLDAEGYLQVTDRIKDVIKTGGEWVSSLQIEDIIARHPAVAETAVIGIQDGKWG 476 Query: 408 ETPCAFIELK---AGIEQPDESEIIAFCRE--RLAHFKCPKQVIF-CELPKTGTGKIQKF 461 E P A + LK A + + D E + E ++ + P +V F EL +T GK+ K Sbjct: 477 ERPVALVVLKKDAAAVSEDDIREHVRAAAEAGAISRYGVPDRVRFVAELARTSVGKLNKR 536 Query: 462 RLRE 465 +RE Sbjct: 537 VMRE 540 >gi|300313115|ref|YP_003777207.1| long-chain-fatty-acid-CoA ligase [Herbaspirillum seropedicae SmR1] Length = 556 Score = 173 bits (439), Expect = 2e-44, Method: Compositional matrix adjust. Identities = 138/468 (29%), Positives = 213/468 (45%), Gaps = 22/468 (4%) Query: 7 NTPAMLESHFGIPLSGAVLNSINCRLDSDGVRFILQHGECKILLVDREFSELVSRAIADM 66 N + ES + G V N R+ ++ Q ++L DR F++ V A Sbjct: 96 NNQQIFESAWAAFKMGVVWVPTNFRITPPEAAYLGQSSGACVMLYDRGFAQYVDAVKAAS 155 Query: 67 PDKPLIVDINDVEAPPGKAIGELDYESLLQEGAPDFEGIWPSDEWDAIALNYTSGTTSDP 126 P +V + D A GELDYE+L++EG+ D D + YTSGTT P Sbjct: 156 PALEHVVALADARA------GELDYEALVREGSGAAFREAEVDYDDPLWFFYTSGTTGHP 209 Query: 127 KGVVPSHRGTYVMSMLQLTDW--GMPRNPVYLWTLPMFHANG-WCFTWAITAAAGTHVCM 183 K + SH + L D G+ L P+ H G AA + Sbjct: 210 KAGMLSHGQMAFVVTNHLADLMPGLTHQSRSLVVAPLSHGAGVHAVINTARGAASILLSS 269 Query: 184 RKVTARNIFDAIADHGVNHFCAAPIVLSSIASAPESEKRPLPHSVRVRTAGSPPPAA-VL 242 ++ + + + V++ P ++ + ++ V AG+P A + Sbjct: 270 ERLVVEEAWQLVEKYRVDNLFTVPTIVKILVEDESVDRYDHSSLKHVIYAGAPMYRADQV 329 Query: 243 KAVLALGFEVEHVYGITEASGTPVSCYINPAWSQYDKDEQSRLMARQGNRSAALEGLMVA 302 A+ LG + YG+ E +G + P + ++ D + AR G G+ +A Sbjct: 330 YALKKLGKVLVQYYGLGEVTG---NITFLPPYLHFEDDAHPQ--ARVGTCGMPRTGMQIA 384 Query: 303 --DPDTLEPVPFDGKTQGELLLKGNIVMKGYLKNEEATENAFAGGWFHTGDVAVVHADGY 360 + D E PF+ GE+ ++G V GY N EA AF WFHTGD+ V DG+ Sbjct: 385 ILNDDGQELAPFE---TGEICVRGPAVFMGYHNNPEANAKAFKHDWFHTGDLGHVDQDGF 441 Query: 361 VQITDRSKDVIISGGENISSVEVEDVLHCHPAVLIAAVVSQPDAKWGETPCAFIELKAGI 420 + IT RS D+ ISGG N+ E+E+ L HPAV AV+ PD KWGE+ A I KAG Sbjct: 442 LYITGRSSDMYISGGSNVYPREIEEALLTHPAVSEVAVLGVPDPKWGESGLAVIVCKAG- 500 Query: 421 EQPDESEIIAFCRERLAHFKCPKQVIFCE-LPKTGTGKIQKFRLRELV 467 +Q D ++A R+ +K P++ I+ + +PK+G GKI K +++ L+ Sbjct: 501 QQVDGEALLAHLESRIGKYKWPRRFIYWDSMPKSGYGKIVKKQIKALL 548 >gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligase [Herbaspirillum seropedicae SmR1] Length = 566 Score = 108 bits (271), Expect = 7e-25, Method: Compositional matrix adjust. Identities = 112/389 (28%), Positives = 169/389 (43%), Gaps = 55/389 (14%) Query: 112 DAIALNYTSGTTSDPKGVVPSHRGTYVMSMLQLTDWGMPR--------NPVYLWTLPMFH 163 D L YT GTT KG V +HR V ++LQ +W P V++ LP++H Sbjct: 206 DIAFLQYTGGTTGVAKGAVLTHR-NLVANVLQAEEWLTPALKAGKPIDQLVFVCALPLYH 264 Query: 164 ANGWCFTWAITAAAGTHVCMRKVTARNIFD------AIADHGVNHFCAAPIVLSSIASAP 217 F + GT + N D +A + VN F A + +++ + Sbjct: 265 ----IFALTVCNMLGTREGALNLLIPNPRDIPGFVKELAKYKVNTFPAVNTLYNALLNNA 320 Query: 218 ESEKRPLPHSVRVRTAGSPPPAAVLKAVL-----ALGFEVEHVYGITEASGTPVSCYINP 272 + + R G AV K+V G + YG++E S P++ NP Sbjct: 321 DFARLDF-SGYRCCVGGG---MAVQKSVADKWKKLTGCPIIEGYGLSETS--PIAS-ANP 373 Query: 273 AWSQYDKDEQSRLMARQGNRSAALEGLMVADPDTLEPVPFDGKTQGELLLKGNIVMKGYL 332 D+ + + A L+ D +PVP GE+ ++G VM GY Sbjct: 374 C--TIDEYTGTIGLPLPSTEFAILD-------DDGQPVPLG--QPGEIAIRGPQVMPGYW 422 Query: 333 KNEEATENAFA-GGWFHTGDVAVVHADGYVQITDRSKDVIISGGENISSVEVEDVLHCHP 391 + + T G+F TGD+ V+ GY +I DR KD+I+ G N+ EVE V+ HP Sbjct: 423 QRPDETAKVMTPDGFFKTGDIGVMDERGYTKIVDRKKDMILVSGFNVYPNEVEGVVAQHP 482 Query: 392 AVLIAAVVSQPDAKWGETPCAFIELKAGIEQPDESEIIAFCRERLAHFKCPKQVIFC-EL 450 VL A V PD GE F+ K + ++++ +C+E+ +K PK + F EL Sbjct: 483 GVLECACVGVPDEHTGEAVKLFVVRKD--KTLSAAQLMDYCKEQFTGYKKPKYIEFRDEL 540 Query: 451 PKTGTGKIQKFRLRELVGSRTAITEPARA 479 PKT GKI + LR+ EPA+A Sbjct: 541 PKTNVGKILRRELRD---------EPAKA 560 >gi|300309365|ref|YP_003773457.1| acetyl-coenzyme A synthetase [Herbaspirillum seropedicae SmR1] Length = 549 Score = 101 bits (252), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 111/380 (29%), Positives = 162/380 (42%), Gaps = 53/380 (13%) Query: 112 DAIALNYTSGTTSDPKGVVPSHRGTYV-MSMLQLTDWGMPRNPVYLWTLPMFHANGWCFT 170 D + YTSGTT KG + +HR + ++++ P+ WT + G Sbjct: 196 DPAMIIYTSGTTGKAKGALHAHRVLLGHLPGVEVSHDSFPQEGDRFWTPADWAWIGGLLD 255 Query: 171 WAI-TAAAGTHVCMR---KVTARNIFDAIADHGVNHFCAAPIVLSSIASAPESEKRPLPH 226 + + G V R K A +F +A H + + P L + A + Sbjct: 256 VLLPSLYHGVAVVARRLEKFDAAEVFGLLARHQIRNVFFPPTALKMLRGAATVRAQA-DF 314 Query: 227 SVRVRTAGSPPPAAVLKA--VLALGFEVEHVYGITEAS---GTPVSCYINPAWSQYDKDE 281 S+R +G L A ALG + YG TE + + CY P+ S Sbjct: 315 SLRSVASGGETLGDDLIAWGREALGVTINEFYGQTECNLVVSSSSHCY--PSVS------ 366 Query: 282 QSRLMARQGNRSAALEGLMVADPDTLEPVPFDGKTQGELL---LKGNIVMKG-------- 330 G+ A+ G +V D QG++L GNI ++ Sbjct: 367 --------GSMGRAVPGHVVQIVDE----------QGQVLPHGTVGNIAIRAPDPVMFLR 408 Query: 331 YLKNEEATENAFAGGWFHTGDVAVVHADGYVQITDRSKDVIISGGENISSVEVEDVLHCH 390 Y +NEEAT FAG + TGD+ + GY++ R+ DVI S G I +E+ L H Sbjct: 409 YWRNEEATREKFAGDFLLTGDLGSMDEQGYIRYLGRNDDVITSAGYRIGPAAIEECLMRH 468 Query: 391 PAVLIAAVVSQPDAKWGETPCAFIELKAGIEQPDE---SEIIAFCRERLAHFKCPKQVIF 447 PAV IAAVV DA E AF+ LK G+ PDE +E+ R +LA + P+ + F Sbjct: 469 PAVRIAAVVGVKDALRTEVVKAFVVLKDGV-TPDEALKAELQQHVRAQLAAHEYPRLISF 527 Query: 448 -CELPKTGTGKIQKFRLREL 466 LP T TGKI + L+E+ Sbjct: 528 VAALPTTATGKIMRKTLKEM 547 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 0.319 0.135 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: 1,547,602 Number of extensions: 65933 Number of successful extensions: 258 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 240 Number of HSP's successfully gapped: 9 Length of query: 479 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 390 Effective length of database: 1,198,455 Effective search space: 467397450 Effective search space used: 467397450 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 (21.7 bits) S2: 132 (55.5 bits)