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_RS19480 AZOBR_RS19480 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__azobra:AZOBR_RS19480 Length = 556 Score = 576 bits (1484), Expect = e-169 Identities = 293/556 (52%), Positives = 382/556 (68%), Gaps = 18/556 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L + AN+ L+PL FL+RAA V+P + ++ HG R T+ Q + R R+FA AL + Sbjct: 16 LAPDPANHVPLSPLSFLKRAAKVYPDKPAIRHGRRTITYAQFHDRVRRFAGALLRAGVRR 75 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G TV+V+APNVPAL EAH+AVP+AGAV+N +N RL+A+ IAF+L HS ++VD+E Sbjct: 76 GDTVSVLAPNVPALLEAHYAVPLAGAVLNALNTRLDAAAIAFILDHSETKLLIVDRELSP 135 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 +A+ AL +P LV I DE A GA+EYE FL DP W Sbjct: 136 VAKAALARTE-------RPITLVEIADEQAPD-----APSLGAVEYEDFLAAADPA-PWH 182 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P+DEWQ+I+L YTSGTT +PKGVV HRGAYL +L + + +++LWTLPMFHCN Sbjct: 183 GPDDEWQAIALNYTSGTTGNPKGVVYHHRGAYLNALGNAFTLNVRPESVFLWTLPMFHCN 242 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GW Y+W + A GT++CLR+V ++ AIA+ GVTH C AP+VLN +++AP P Sbjct: 243 GWTYSWAVTAAGGTHVCLRRVEPAAIFDAIAELGVTHLCGAPIVLNMLIHAPAAVRR-PA 301 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 P V V T GAAPP +VL M+ GF+V H YGL+E YGP+T+CA + W+ L A Sbjct: 302 PRRVIVGTGGAAPPSAVLAGMATLGFEVVHMYGLTECYGPATVCAPQDGWEDLDADGLAL 361 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 ARQGV ++A+E V+D +T +PVPAD T+GEI +RGN VMKGYLKNP A +E+ D Sbjct: 362 QFARQGVNHVAVEDATVLDRETGRPVPADAQTIGEIALRGNTVMKGYLKNPAATKEALKD 421 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWF +GDL V HPDGYIE+KDRSKDIIISGGENISSLEVE LY HPAVLE +VVARPD+ Sbjct: 422 GWFRTGDLGVLHPDGYIEVKDRSKDIIISGGENISSLEVEEALYRHPAVLEAAVVARPDD 481 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 RWGESPCAFVT+KP ++ +E DII++C+ ++ Y VP++VVF LPKT+TGKIQK Sbjct: 482 RWGESPCAFVTVKPGAERPSE----SDIIQWCRDRIAHYKVPRTVVFSDLPKTSTGKIQK 537 Query: 551 HVLRAKAKEMGALKKS 566 VLR A+E+G +++ Sbjct: 538 TVLRDAARELGERREA 553 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: 37 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: 556 Length adjustment: 36 Effective length of query: 532 Effective length of database: 520 Effective search space: 276640 Effective search space used: 276640 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