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 WP_043744440.1 AMB_RS12570 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >NCBI__GCF_000009985.1:WP_043744440.1 Length = 544 Score = 611 bits (1576), Expect = e-179 Identities = 294/550 (53%), Positives = 384/550 (69%), Gaps = 18/550 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L KN ANY LTPL FLER+A+V+P R SV+HG +TW QTY RCR+ SAL +G+ Sbjct: 11 LDKNPANYVPLTPLGFLERSASVYPDRISVVHGDLRFTWKQTYDRCRRLGSALAARGVGV 70 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G TVAV+A N PA YEA F VPM G V+ +NIRL+A IAF+L H A ++ D+EF Sbjct: 71 GDTVAVMAANTPAAYEAAFGVPMTGGVLCALNIRLDAEAIAFMLQHGEAKVLLTDREFAP 130 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 ++AL +L E+K P+++ I D + + G +EYE F+ GGDPE+ W Sbjct: 131 TIKKALSLL--EAK-----PIVIDIDDAAVTTGEM-----LGEMEYEAFIAGGDPEYAWV 178 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P DEW +I+L YTSGTT +PKGVV HRGAY+ +L V WG+ +YLWTLPMFHCN Sbjct: 179 WPSDEWDAIALNYTSGTTGNPKGVVYHHRGAYINALGNVVNWGMTGHPVYLWTLPMFHCN 238 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GWC+ W +AA GTN+CLR+V +++AI K+ VTH C AP+V+ ++NAP ++ PL Sbjct: 239 GWCFPWTLAALAGTNVCLRRVDGGHMFAAIEKHKVTHMCGAPIVMGMLINAPEKDRR-PL 297 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 PH V MTA A PP +V+ + +GFK+ H YGL+E YGP+T+CAWK EWD LP ++A+ Sbjct: 298 PHPVEFMTAAAPPPAAVIGRLESQGFKITHVYGLTEVYGPATVCAWKEEWDELPLDERAK 357 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 + +RQGVRY+ E + V D ++ PVP DG TMGE+ RGN VMKGYLKNP A E+F+ Sbjct: 358 MKSRQGVRYVNEEAMMVADPVSLVPVPKDGATMGEVFYRGNVVMKGYLKNPSATNEAFSG 417 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWFH+GDL V H DGYIE+KDRSKDIIISGGENIS++EVE LY HP+V E +VVARPDE Sbjct: 418 GWFHTGDLGVWHADGYIELKDRSKDIIISGGENISTIEVEGVLYQHPSVGEAAVVARPDE 477 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 +WGE+PCAF+ L K AE+I+ FC+ ++ Y P++VVF LPKT+TGK+QK Sbjct: 478 KWGETPCAFIGL-----KDGATATAEEIMAFCRERLAHYKCPRTVVFTNLPKTSTGKVQK 532 Query: 551 HVLRAKAKEM 560 +VLR AK++ Sbjct: 533 YVLREMAKKL 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: 951 Number of extensions: 35 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: 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