Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate AZOBR_RS09405 AZOBR_RS09405 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__azobra:AZOBR_RS09405 Length = 544 Score = 541 bits (1393), Expect = e-158 Identities = 269/549 (48%), Positives = 362/549 (65%), Gaps = 15/549 (2%) Query: 10 DLPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIG 69 +L + AN+ LTPL FL R+A V+P +T+V++G +WL+ HR R ASA++ + Sbjct: 9 ELSRRTANHVPLTPLDFLRRSAMVYPDKTAVVYGPLRRSWLEVEHRARALASAVSRAGVR 68 Query: 70 LGSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFF 129 G V+V+A N PA+ EAHF VP AGAV+N +N RL+ +AF+L H+ + +VD+ Sbjct: 69 PGEVVSVLAFNTPAMLEAHFGVPGAGAVLNAINTRLDPPAVAFILEHAESRLFLVDRGLS 128 Query: 130 SLAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDW 189 ++A AL+ + PP +V I D + A G +EYE FL+ GDPE W Sbjct: 129 AVARAALERMTA-------PPRVVWIDDPAAQD-----ADPVGDLEYEDFLKTGDPEAPW 176 Query: 190 KPPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHC 249 + PEDEW+SI+L YTSGTT +PKGV+ HRGA+L +L + +G+ ++YLWTLPMFHC Sbjct: 177 RRPEDEWESIALNYTSGTTGNPKGVLYHHRGAHLNALGNVITFGLRPDSVYLWTLPMFHC 236 Query: 250 NGWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIP 309 NGW Y W + A T++CLR V ++ IA+ VTH C APVVL +++AP Sbjct: 237 NGWTYPWAVTAVGATHVCLRAVDPAAIFRLIAEEKVTHLCGAPVVLTMLIHAPDAVKRAF 296 Query: 310 LPHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQA 369 V V T GAAPP +V+ M GF++ H YG++E YGPST CAW+ W LP ++A Sbjct: 297 DHGPVQVATGGAAPPSAVIAGMERMGFRLTHLYGMTECYGPSTGCAWQEAWAELPLEERA 356 Query: 370 RLNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFA 429 ARQGV + + V+D T + VPADG T+GE+ +RGN VMKGYLKNP A +E+ Sbjct: 357 VKMARQGVPNVTMSEQTVLDPDTGREVPADGETLGELALRGNTVMKGYLKNPAATDEALR 416 Query: 430 DGWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPD 489 DGW H+GDLAV HPD Y+EIKDR+KDIIISGGENI+SLEVE LY HP V+E +VVARPD Sbjct: 417 DGWLHTGDLAVLHPDRYVEIKDRAKDIIISGGENIASLEVEEVLYKHPHVMEAAVVARPD 476 Query: 490 ERWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQ 549 +WGE+PCAFVTLKP S +V ++I +C+ + + P++VVFG LPKT+TGKIQ Sbjct: 477 AKWGETPCAFVTLKPG---SEGRVSEAEVIGWCRDHLAHFKTPRTVVFGALPKTSTGKIQ 533 Query: 550 KHVLRAKAK 558 K VLR +A+ Sbjct: 534 KFVLREQAR 542 Lambda K H 0.318 0.134 0.415 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 888 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 568 Length of database: 544 Length adjustment: 36 Effective length of query: 532 Effective length of database: 508 Effective search space: 270256 Effective search space used: 270256 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory