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= 0005.0258.p (397 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313115|ref|YP_003777207.1| long-chain-fatty-acid-CoA ligas... 245 4e-66 gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligas... 166 4e-42 gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid li... 147 1e-36 gi|300309365|ref|YP_003773457.1| acetyl-coenzyme A synthetase [H... 138 9e-34 gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA lig... 114 1e-26 >gi|300313115|ref|YP_003777207.1| long-chain-fatty-acid-CoA ligase [Herbaspirillum seropedicae SmR1] Length = 556 Score = 245 bits (626), Expect = 4e-66, Method: Compositional matrix adjust. Identities = 144/374 (38%), Positives = 208/374 (55%), Gaps = 13/374 (3%) Query: 26 SGPLLDAFPIAADALAWLFYTSGTTGRPKGVMLTHANMVSMAMHFLIDVQP-LASDDVLI 84 SG + D W FYTSGTTG PK ML+H M + + L D+ P L + Sbjct: 182 SGAAFREAEVDYDDPLWFFYTSGTTGHPKAGMLSHGQMAFVVTNHLADLMPGLTHQSRSL 241 Query: 85 HVAPMSHGSGLYSVPYFIRGGLQVIPESGGLDEAELFGLLNHYDKASLFAAPTIVMRLIQ 144 VAP+SHG+G+++V RG ++ S L E + L+ Y +LF PTIV L++ Sbjct: 242 VVAPLSHGAGVHAVINTARGAASILLSSERLVVEEAWQLVEKYRVDNLFTVPTIVKILVE 301 Query: 145 HVR----NHTGVTWPGLRCLLVGGAPFYAEDIKSAVQCFGARVAQLYGQGETPMTISALS 200 +H+ L+ ++ GAP Y D A++ G + Q YG GE I+ L Sbjct: 302 DESVDRYDHSS-----LKHVIYAGAPMYRADQVYALKKLGKVLVQYYGLGEVTGNITFLP 356 Query: 201 ADLLARAVAADDTAMLVSVGFAQTAIGITIVDADGNPVTAGTPGEVIVRGPTVMTGYWGN 260 L A A + + G +T + I I++ DG + GE+ VRGP V GY N Sbjct: 357 P-YLHFEDDAHPQARVGTCGMPRTGMQIAILNDDGQELAPFETGEICVRGPAVFMGYHNN 415 Query: 261 PEATRQTIGGGALRTGDIGLIDERGLLHLKDRSKDVIISGGTNIYPREVEEALLTHPAVE 320 PEA + TGD+G +D+ G L++ RS D+ ISGG+N+YPRE+EEALLTHPAV Sbjct: 416 PEANAKAFKHDWFHTGDLGHVDQDGFLYITGRSSDMYISGGSNVYPREIEEALLTHPAVS 475 Query: 321 EVSVVGAPDPEWGESVVAFIVCHAGASA-GEQELDELCIRTIARFKRPKRYVFVEKLPKN 379 EV+V+G PDP+WGES +A IVC AG GE L L R I ++K P+R+++ + +PK+ Sbjct: 476 EVAVLGVPDPKWGESGLAVIVCKAGQQVDGEALLAHLESR-IGKYKWPRRFIYWDSMPKS 534 Query: 380 GTGKVLKRELQQTL 393 G GK++K++++ L Sbjct: 535 GYGKIVKKQIKALL 548 >gi|300313157|ref|YP_003777249.1| long-chain-fatty-acid-CoA ligase [Herbaspirillum seropedicae SmR1] Length = 566 Score = 166 bits (419), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 118/381 (30%), Positives = 174/381 (45%), Gaps = 27/381 (7%) Query: 22 LDAASGPLLDAFPIAADALAWLFYTSGTTGRPKGVMLTHANMVSMAMHFLIDVQPLASDD 81 L A G L + D +A+L YT GTTG KG +LTH N+V+ + + P Sbjct: 189 LSQARGKTLQPVTLTHDDIAFLQYTGGTTGVAKGAVLTHRNLVANVLQAEEWLTP----- 243 Query: 82 VLIHVAPMSHGSGLYSVPYFIRGGLQVIPESGGLDEAELFGLLNHYD-----------KA 130 L P+ + ++P + L V G + A + N D K Sbjct: 244 ALKAGKPIDQLVFVCALPLYHIFALTVCNMLGTREGALNLLIPNPRDIPGFVKELAKYKV 303 Query: 131 SLFAAPTIVMRLIQHVRNHTGVTWPGLRCLLVGGAPFYAEDIKSAVQCFGARVAQLYGQG 190 + F A + + + + + + G RC + GG + G + + YG Sbjct: 304 NTFPAVNTLYNALLNNADFARLDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIEGYGLS 363 Query: 191 ETPMTISALSADLLARAVAADDTAMLVSVGFAQTAIGITIVDADGNPVTAGTPGEVIVRG 250 ET SA D+ ++G + I+D DG PV G PGE+ +RG Sbjct: 364 ETSPIASA-------NPCTIDEYTG--TIGLPLPSTEFAILDDDGQPVPLGQPGEIAIRG 414 Query: 251 PTVMTGYWGNPEATRQTIG-GGALRTGDIGLIDERGLLHLKDRSKDVIISGGTNIYPREV 309 P VM GYW P+ T + + G +TGDIG++DERG + DR KD+I+ G N+YP EV Sbjct: 415 PQVMPGYWQRPDETAKVMTPDGFFKTGDIGVMDERGYTKIVDRKKDMILVSGFNVYPNEV 474 Query: 310 EEALLTHPAVEEVSVVGAPDPEWGESVVAFIVCHAGASAGEQELDELCIRTIARFKRPKR 369 E + HP V E + VG PD GE+V F+V + Q +D C +K+PK Sbjct: 475 EGVVAQHPGVLECACVGVPDEHTGEAVKLFVVRKDKTLSAAQLMD-YCKEQFTGYKKPKY 533 Query: 370 YVFVEKLPKNGTGKVLKRELQ 390 F ++LPK GK+L+REL+ Sbjct: 534 IEFRDELPKTNVGKILRRELR 554 >gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid ligase II protein [Herbaspirillum seropedicae SmR1] Length = 546 Score = 147 bits (372), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 120/370 (32%), Positives = 180/370 (48%), Gaps = 25/370 (6%) Query: 38 DALAWLFYTSGTTGRPKGVMLTHA----NMVSMAMHFLIDVQPLASDDVLIHVAPMSHGS 93 DA+A L YTSGTTG PKGV+ H N VS + + + P V + PM H + Sbjct: 184 DAIA-LNYTSGTTGDPKGVVYHHRGAALNAVSNILEWDLPKHP-----VYLWTLPMFHCN 237 Query: 94 GLYSVPYFI--RGGLQVIPESGGLDEAELFGLLNHYDKASLFAAPTIVMRLIQHVRN-HT 150 G + P+ + R G+ V + +F L+ + AAP + L Sbjct: 238 G-WCFPWTVAARAGVNVCLRK--FEPKLVFDLIAEHGITHYCAAPIVHAALANAPEGWRA 294 Query: 151 GVTWPGLRCLLVGGAPFYAEDIKSAVQCFGARVAQLYGQGETPMTISALSADLLARAVAA 210 G+ P ++ ++ G P A + + ++ + +YG E + + ++ Sbjct: 295 GIRGP-VKAMVAGAPPPAA--VLAKMEAMQFELTHVYGLTEVYGPAAVCAEQDEWNTLSV 351 Query: 211 DDTAMLVSVGFAQTAI--GITIVDADG-NPVTAGTP--GEVIVRGPTVMTGYWGNPEATR 265 D A+ S + + G+T++ D PV A GE++ RG M GY N AT Sbjct: 352 DQRAVQKSRQGVRYHLQSGVTVLSPDTMAPVAADGEEIGEIMFRGNICMKGYLKNDRATH 411 Query: 266 QTIGGGALRTGDIGLIDERGLLHLKDRSKDVIISGGTNIYPREVEEALLTHPAVEEVSVV 325 + GG TGD+G+++ G + +KDRSKD+IISGG NI EVE+ L HPAV +VV Sbjct: 412 EAFAGGWFHTGDLGVMNADGYIKIKDRSKDIIISGGENISSVEVEDVLYRHPAVLAAAVV 471 Query: 326 GAPDPEWGESVVAFIVCHAGASAGEQELDELCIRTIARFKRPKRYVFVEKLPKNGTGKVL 385 PD +WGE+ AF+ GA G EL E C +A FK PK ++ LPK TGK+ Sbjct: 472 AQPDEKWGETPCAFVELKEGAEVGAAELTEFCRSHLAGFKVPKA-IYFGPLPKTSTGKIQ 530 Query: 386 KRELQQTLAN 395 K EL++ + + Sbjct: 531 KFELRKRMKS 540 >gi|300309365|ref|YP_003773457.1| acetyl-coenzyme A synthetase [Herbaspirillum seropedicae SmR1] Length = 549 Score = 138 bits (347), Expect = 9e-34, Method: Compositional matrix adjust. Identities = 114/372 (30%), Positives = 166/372 (44%), Gaps = 22/372 (5%) Query: 30 LDAFPIAADALAWLFYTSGTTGRPKGVMLTHANMVSMAMHFLIDVQPLASD-DVLIHVAP 88 LD AD A + YTSGTTG+ KG + H ++ + + D A Sbjct: 187 LDPVLTLADDPAMIIYTSGTTGKAKGALHAHRVLLGHLPGVEVSHDSFPQEGDRFWTPAD 246 Query: 89 MSHGSGLYSV--PYFIRGGLQVIPESGGLDEAELFGLLNHYDKASLFAAPTIV--MRLIQ 144 + GL V P G V D AE+FGLL + ++F PT + +R Sbjct: 247 WAWIGGLLDVLLPSLYHGVAVVARRLEKFDAAEVFGLLARHQIRNVFFPPTALKMLRGAA 306 Query: 145 HVRNHTGVTWPGLRCLLVGGAPFYAEDIKSAVQCFGARVAQLYGQGETPMTISALSADLL 204 VR + LR + GG + I + G + + YGQ E + +S+ S Sbjct: 307 TVRAQADFS---LRSVASGGETLGDDLIAWGREALGVTINEFYGQTECNLVVSSSSHCY- 362 Query: 205 ARAVAADDTAMLVSVGFAQTAIGITIVDADGNPVTAGTPGEVIVRGP--TVMTGYWGNPE 262 ++ S+G A + IVD G + GT G + +R P + YW N E Sbjct: 363 --------PSVSGSMGRAVPGHVVQIVDEQGQVLPHGTVGNIAIRAPDPVMFLRYWRNEE 414 Query: 263 ATRQTIGGGALRTGDIGLIDERGLLHLKDRSKDVIISGGTNIYPREVEEALLTHPAVEEV 322 ATR+ G L TGD+G +DE+G + R+ DVI S G I P +EE L+ HPAV Sbjct: 415 ATREKFAGDFLLTGDLGSMDEQGYIRYLGRNDDVITSAGYRIGPAAIEECLMRHPAVRIA 474 Query: 323 SVVGAPDPEWGESVVAFIVCHAGASAGE---QELDELCIRTIARFKRPKRYVFVEKLPKN 379 +VVG D E V AF+V G + E EL + +A + P+ FV LP Sbjct: 475 AVVGVKDALRTEVVKAFVVLKDGVTPDEALKAELQQHVRAQLAAHEYPRLISFVAALPTT 534 Query: 380 GTGKVLKRELQQ 391 TGK++++ L++ Sbjct: 535 ATGKIMRKTLKE 546 >gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA ligase [Herbaspirillum seropedicae SmR1] Length = 545 Score = 114 bits (285), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 105/367 (28%), Positives = 164/367 (44%), Gaps = 37/367 (10%) Query: 53 PKGVMLTHANMVSMAMHFLIDVQPLA---------SDDVLIHVAPMSHGSGLYSVPYF-- 101 PKGV +H +V +H L LA DDV + + PM H + +PY Sbjct: 193 PKGVYFSHRQLV---LHTLATTAGLALAPQQGRFHRDDVYMPLTPMFHVHA-WGLPYVAT 248 Query: 102 IRGGLQVIPESGGLDEAELFGLLNHYDKASLFAAPTIVMRLI--QHVRNHTGVTWPGLRC 159 + G QV P G + L+ PTI+ ++ + R W Sbjct: 249 MAGVKQVYP--GRYVPDTICRLIREEKVTFSHCVPTILQMVLTSEQAREADLSGWK---- 302 Query: 160 LLVGGAPFYAEDIKSAVQCFGARVAQLYGQGETP--MTISALSADLLARAVAADDTAMLV 217 +++GG+ K A + G V YG ET +T++ + + L + A+ V Sbjct: 303 MIIGGSAMTGSLAKMA-RDRGIDVFTGYGMSETCPVLTLAQVPTEELG---GEREAAIRV 358 Query: 218 SVGFAQTAIGITIVDADGN--PVTAGTPGEVIVRGPTVMTGYWGNPEATRQTIGGGALRT 275 G + + VD + P T GEV+VR P + GY EA+ + GG L T Sbjct: 359 KTGRPLPLVDLRTVDGEMQDCPRDGSTTGEVVVRAPWLTQGYLHQAEASEELWRGGWLHT 418 Query: 276 GDIGLIDERGLLHLKDRSKDVIISGGTNIYPREVEEALLTHPAVEEVSVVGAPDPEWGES 335 DIG +D G L + DR KDVI +GG + ++E+ + HPAV E +V+G D +WGE Sbjct: 419 QDIGHLDAEGYLQVTDRIKDVIKTGGEWVSSLQIEDIIARHPAVAETAVIGIQDGKWGER 478 Query: 336 VVAFIVCHAGASAGEQELDELCIR------TIARFKRPKRYVFVEKLPKNGTGKVLKREL 389 VA +V A+A ++ +R I+R+ P R FV +L + GK+ KR + Sbjct: 479 PVALVVLKKDAAAVSEDDIREHVRAAAEAGAISRYGVPDRVRFVAELARTSVGKLNKRVM 538 Query: 390 QQTLANT 396 ++ ++ Sbjct: 539 REQYPSS 545 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 0.137 0.410 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: 1,344,983 Number of extensions: 60542 Number of successful extensions: 215 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 177 Number of HSP's successfully gapped: 18 Length of query: 397 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 310 Effective length of database: 1,207,925 Effective search space: 374456750 Effective search space used: 374456750 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: 131 (55.1 bits)