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_011385011.1 AMB_RS13240 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >NCBI__GCF_000009985.1:WP_011385011.1 Length = 541 Score = 577 bits (1488), Expect = e-169 Identities = 290/552 (52%), Positives = 373/552 (67%), Gaps = 22/552 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L +NAAN+ ALTPL FLERAA V P R +VIHG TW +T+ RCR+ A+AL IGL Sbjct: 10 LDRNAANFVALTPLTFLERAAAVWPDRLAVIHGPVRRTWAETFVRCRKLAAALTARGIGL 69 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G TVA++ N P +EAHF VP+ GAV+N +N RL+A I F+L H+ A ++ D+EF Sbjct: 70 GDTVALMGANTPETFEAHFGVPLTGAVLNAINTRLDADAITFILNHAEAKILITDREFSP 129 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 + ++AL L + P++ + D + G YE+ L+ E W Sbjct: 130 VVKKALAALGRTI------PVIDI------DDPQFKGGELLGEKNYEQLLDEAASEAPWT 177 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P DEWQ+I+L YTSGTT +PKGVV HRGA+L ++S ++ W + + +YLWTLPMFHCN Sbjct: 178 LPTDEWQAIALNYTSGTTGNPKGVVYHHRGAHLNAVSNALSWQMGDNTVYLWTLPMFHCN 237 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPP--EEAII 308 GWC+ W MA GT++CLR V + AI VT+FC AP+VLN I NAP +E I Sbjct: 238 GWCFPWTMAVVAGTSVCLRHVRVDAIMGAIRDEKVTNFCGAPIVLNMINNAPAALKEGI- 296 Query: 309 PLPHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQ 368 H V VMTAGAAPP V+ M G++V H YGL+E YGP+ C W +W+ L ++ Sbjct: 297 --SHAVKVMTAGAAPPAPVIAGMERMGWEVTHVYGLTECYGPTVQCVWHDKWNGLSIDEK 354 Query: 369 ARLNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESF 428 A++ ARQGVR LEGL + D +++P P DG T+GEI MRGN VMKGYLKN KA EE+F Sbjct: 355 AQIKARQGVRGPMLEGLMIADPISLEPAPKDGKTVGEIFMRGNNVMKGYLKNEKATEEAF 414 Query: 429 ADGWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARP 488 A GWFH+GDLAV HPDGYIEIKDRSKDIIISGGENISS+EVE+ LY H AVLE +VVARP Sbjct: 415 AGGWFHTGDLAVCHPDGYIEIKDRSKDIIISGGENISSIEVEDILYAHLAVLEAAVVARP 474 Query: 489 DERWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKI 548 DE+WGE+PCAF+ LK + + DII FC+ +M + VP+++VFG LPKT+TGK+ Sbjct: 475 DEKWGETPCAFIALKDGAEATE-----ADIITFCRERMAHFKVPRTIVFGGLPKTSTGKV 529 Query: 549 QKHVLRAKAKEM 560 QK +LR KAKE+ Sbjct: 530 QKFMLRQKAKEL 541 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: 846 Number of extensions: 37 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: 541 Length adjustment: 36 Effective length of query: 532 Effective length of database: 505 Effective search space: 268660 Effective search space used: 268660 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