Align 2-methylpropanoate--CoA ligase CCL4; HlCCL4; 2-methylbutanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate WP_028315795.1 G491_RS0119705 fatty acid--CoA ligase
Query= SwissProt::M4IQQ5 (556 letters) >NCBI__GCF_000429905.1:WP_028315795.1 Length = 544 Score = 267 bits (682), Expect = 9e-76 Identities = 175/540 (32%), Positives = 288/540 (53%), Gaps = 32/540 (5%) Query: 16 PLGFLERAATVYGDCTSVVY-DAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNV 74 PL + AT+Y +VY D ++YT+ +R LA+++ LGI G V+V+ + Sbjct: 16 PLLIKQLLATIYEPDQEIVYRDKMTYTYKDMEKRTRKLANALEGLGITQGSTVAVMDWDS 75 Query: 75 PQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPK 134 + E FAVPM GA+L+ +N+RL + ++H+E +I V H +LEA+ + Sbjct: 76 HRYLECFFAVPMMGAVLHTINIRLSPEQLVYTVNHAEDDIILV-HKDFAPLLEAVK--DQ 132 Query: 135 QAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI-LNYTS 193 V + V +AD ++ +S EF Y+DL++ +++W P + + M + YT+ Sbjct: 133 LTTVKKFVLIADYEDAPATS---LEFAGEYEDLVEAAGEEYEW--PDFDENAMATMFYTT 187 Query: 194 GTTSSPKGVVHCHRGIFIMTVDSL-----------IDWGVPKQPVYLWTLPMFHANGWSY 242 GTT PKGV HR + + T + ID G VY+ PMFH + W Sbjct: 188 GTTGLPKGVYFSHRQLVLHTFGLMSAANSFRAQLKIDAG----DVYMPLTPMFHVHAWGM 243 Query: 243 PWGMAAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEPLKTTV-QI 301 P+ M +G I +++ E+I + + + V+ P +L+ML N+P ++ + ++ Sbjct: 244 PYSMTVMGAKQIYPGRYEPELILKLYRDYKVSFSHCVPTILHMLLNSPSAKDTDFSGWKM 303 Query: 302 MTAGAPPPSAVLFRTESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQG 361 + GA P + LG + YG++ET L+ K LP E+ +++ G Sbjct: 304 IIGGAALPKGMCIEGLKLGINIYSAYGMSETCPLLTQALLKPNMLDLPLEEQVVYRTKTG 363 Query: 362 VGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYT 421 + ++ VVDP G + DG T GEVV+R + GYL +PE ++ + GW +T Sbjct: 364 L-PCPGVQLRVVDPA-GNPLPHDGKTAGEVVVRAPWLTQGYLNNPE-KSEELWEKGWLHT 420 Query: 422 GDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGET 481 GDVG++ GYL+I DR KDVI +GGE LSS+E+ESI+ H + E AVV D+ WGE Sbjct: 421 GDVGIIDELGYLQITDRIKDVIKTGGEWLSSLELESIISQHKGVSEVAVVGVKDDKWGER 480 Query: 482 PCAFVSLKKG--LTKKPTEKEIVEYCRS-KLPRYMVPKTVVFKEELPKTSTGKVQKFILR 538 P A + K+G L+K+ + + + + +P+Y +P++++F +E+PKTS GK+ K +R Sbjct: 481 PMALIVPKEGQELSKEEVQTFMGAWVENGAIPKYGIPESILFVDEIPKTSVGKIDKKEIR 540 Lambda K H 0.319 0.135 0.412 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: 800 Number of extensions: 41 Number of successful extensions: 8 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: 556 Length of database: 544 Length adjustment: 36 Effective length of query: 520 Effective length of database: 508 Effective search space: 264160 Effective search space used: 264160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Jul 25 2024. The underlying query database was built on Jul 25 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