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_011842442.1 RSPH17029_RS17960 AMP-binding protein
Query= SwissProt::M4IS88 (568 letters) >NCBI__GCF_000015985.1:WP_011842442.1 Length = 520 Score = 211 bits (537), Expect = 6e-59 Identities = 157/527 (29%), Positives = 248/527 (47%), Gaps = 45/527 (8%) Query: 35 PTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGLGSTVAVIAPNVPALYEAHFAVPMA 94 P ++I R +W + + L + GS VAV+ N +A+ Sbjct: 24 PDSAALIFRGRTRSWAEFAADMARIQQGLAAQGVRRGSRVAVLDRNSDDYVLLGYALAGM 83 Query: 95 GAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFSLAEEALKILAQESKSHYKPPLLVV 154 GAV+ VN+ L + ++++LG+ ++ EF A EA+ LA PP LV+ Sbjct: 84 GAVLAPVNMWLRPAELSYILGNCQPLLLVTSAEFLDAAREAIAPLAD-------PPALVL 136 Query: 155 IGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWKPPEDEWQSISLGYTSGTTASPKGV 214 GDE+ P T+ +A + G+ PE + YTSGTT PKG Sbjct: 137 RGDEA--PGTIAWAE----------IAAGEGRAPVSRPESWDDPHLVLYTSGTTGRPKGA 184 Query: 215 VLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCNGWCYTWGMAAFCGTNICLRQVTAK 274 ++SHR L +L+A V+GI + + +P+FH W Y G + + A Sbjct: 185 LISHRRTVLDALAALPVFGIGQHERFFCYMPLFHTGAWDYLKLYFMRRGAAVIAERFEAD 244 Query: 275 GVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPLPHLVHVMTAGAAPPPSVLFAMSE- 333 + I + P+VL +V + + + + A P +L + Sbjct: 245 AAVAEIEAHRCNGMFGVPLVLRQMVESQAW-GTSDMSSMRLIAYANYDPSALILRIVEAF 303 Query: 334 -----KGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQARLNARQGVRYIALEGLDVV 388 +G ++A+ YGL+E G IC +PE P L+ Q V + + LD Sbjct: 304 RERGAEGLRIANAYGLTE--GGPYICINRPETAMSKP-----LSIGQPVPGVQVALLD-- 354 Query: 389 DTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFADGWFHSGDLAVKHPDGYIE 448 + ++ VP +GEI +RG A+M GYL P+A E+FA GW H+GDL +G++ Sbjct: 355 --EDLREVPPGA--LGEICVRGPALMSGYLNRPEATAEAFAGGWLHTGDLGRVDEEGFVH 410 Query: 449 IKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDERWGESPCAFVTLKPNIDK 508 + DR KD+I +GGEN+ + EVE TL HPA+ + +VV PD+ +GE A V +P D Sbjct: 411 LVDRKKDMIRTGGENVFAKEVEQTLVTHPAIRDCAVVGLPDDDYGERVVAVVVAEPGTDL 470 Query: 509 SNEQVLAEDIIKFCKSKMPAYWVPKSVVFGP-LPKTATGKIQKHVLR 554 + +V + F + ++ + P+ V+F P LPKT GKI+KH +R Sbjct: 471 AEAEVRS-----FVRDRLAGFKAPRQVIFVPELPKTPAGKIKKHEVR 512 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: 701 Number of extensions: 45 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: 520 Length adjustment: 35 Effective length of query: 533 Effective length of database: 485 Effective search space: 258505 Effective search space used: 258505 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: 52 (24.6 bits)
This GapMind analysis is from Apr 16 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