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_RS06255 AZOBR_RS06255 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__azobra:AZOBR_RS06255 Length = 551 Score = 610 bits (1572), Expect = e-179 Identities = 294/555 (52%), Positives = 382/555 (68%), Gaps = 16/555 (2%) Query: 10 DLPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIG 69 DL +NAAN L+PL FL R A V+P R +VIHG TW +TY RC + ASAL IG Sbjct: 12 DLDQNAANTVPLSPLSFLRRTAAVYPQRIAVIHGPVRRTWAETYERCVRLASALAKRGIG 71 Query: 70 LGSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFF 129 LG TVAV+APN P +EAHF VPM GAV+N +NIRL+A +AF+L H A ++ D+EF Sbjct: 72 LGDTVAVMAPNTPESFEAHFGVPMTGAVLNALNIRLDAEALAFILEHGEAKVLLTDREFS 131 Query: 130 SLAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDW 189 + +A+ +L + + P+++ I D L G YE+FLE GDP ++W Sbjct: 132 GVISKAVHMLEPKRR-----PIVIDIDDPQAKGGEL-----IGEQTYEQFLETGDPAYEW 181 Query: 190 KPPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHC 249 P DEWQ+I+L YTSGTT +PKGVV HRGAYL ++ + W + +YLWTLPMFHC Sbjct: 182 PMPADEWQAIALNYTSGTTGNPKGVVYHHRGAYLNAMGNVLTWAMPHHPVYLWTLPMFHC 241 Query: 250 NGWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIP 309 NGWC+ W + A GTN+C+R +TAKG+Y A+A GVTH C AP+++ IVNAP E+ Sbjct: 242 NGWCFPWTVTAMAGTNVCVRTITAKGIYDALADLGVTHMCGAPIIMGLIVNAP-EDQKRE 300 Query: 310 LPHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQA 369 +P V +MTAGAAPP +V+ + GF V H YGL+E YGP TICAW W+ LP ++A Sbjct: 301 IPRGVKMMTAGAAPPAAVIEKIERMGFDVTHVYGLTEVYGPVTICAWHEHWNDLPLEERA 360 Query: 370 RLNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFA 429 L ARQGV Y LEGL V D T++P DG TMGEI MRGN VMKGYLKNP+A +E+F+ Sbjct: 361 ALKARQGVNYATLEGLMVADPNTLQPTRKDGVTMGEIFMRGNTVMKGYLKNPRATQEAFS 420 Query: 430 DGWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPD 489 GWFH+GDL V H DGYIE+KDRSKDIIISGGENIS++EVE+ LY HP ++E +VVARPD Sbjct: 421 GGWFHTGDLGVWHADGYIELKDRSKDIIISGGENISTIEVESVLYKHPDIVEAAVVARPD 480 Query: 490 ERWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQ 549 E+WGE+PCAFVT+ K +Q+ ++I +C+ + + P++VVF LPKT+TGKIQ Sbjct: 481 EKWGETPCAFVTV-----KEGKQLTEAEVIAYCREHLAHFKCPRTVVFTALPKTSTGKIQ 535 Query: 550 KHVLRAKAKEMGALK 564 K+VLR +A+ + K Sbjct: 536 KYVLRDQARALNGAK 550 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: 911 Number of extensions: 29 Number of successful extensions: 4 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: 551 Length adjustment: 36 Effective length of query: 532 Effective length of database: 515 Effective search space: 273980 Effective search space used: 273980 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