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 GFF3502 PGA1_c35550 medium-chain-fatty-acid--CoA ligase AlkK
Query= SwissProt::M4IQQ5 (556 letters) >FitnessBrowser__Phaeo:GFF3502 Length = 539 Score = 209 bits (532), Expect = 2e-58 Identities = 149/505 (29%), Positives = 244/505 (48%), Gaps = 21/505 (4%) Query: 41 TWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDA 100 TW LA+++ LGI G +A N + E++F V G + + +N RL Sbjct: 41 TWGDIDANARKLAAALGRLGIAQGARCGTIAWNNRRHLEIYFGVSGGGYVCHTINPRLKP 100 Query: 101 RTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEF 160 + +++H+E +++F+D + A+A Q + + + ++ ++++ Sbjct: 101 EQLIYIINHAEDQVLFID----TTFVPAVAQLRAQFTTVQHIVVMGPKDADIAAQIEGVL 156 Query: 161 FCSYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW 220 F Y D++D + W E P L YTSGTT +PKGV + HR + T+ Sbjct: 157 F--YDDVLDAEAAGYDWP-DLDENLPSSLCYTSGTTGNPKGVEYTHRTSVLHTIGGNQPD 213 Query: 221 GVP--KQPVYLWTLPMFHANGWSYPWGMAAVGGTNICLRK-FDSEIIYDMIKRHGVTHMC 277 G+ + L +PMFH N W P+ AAVG + D + +I VT Sbjct: 214 GLALRARDTVLAVVPMFHVNAWGTPYMTAAVGAKLVLPGPHLDGVSLARLIDAEKVTVAL 273 Query: 278 GAPVV-LNMLSNAPGSEPLKTTVQIMTAGAPPPSAVLFRT--ESLGFAVSHGYGLTETAG 334 G P + + +L + +++ G V+ T + G + H +G+TET+ Sbjct: 274 GVPTIWMGLLQGLEETGCTAESLERTIVGGSALPTVMIPTFRDKYGVDLVHAWGMTETSP 333 Query: 335 LVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLR 394 + ++ N L A +A+L+ QG + + +VD +GA + DG T G + + Sbjct: 334 IGTLNQLLQKHNELDAEAQAKLREGQG-RPMYGIDLRIVDD-SGAVLPHDGETQGNLQIC 391 Query: 395 GGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVE 454 G V+ Y + E ++T DGWF TGDV + DGY+ I+DRSKD+I SGGE +S+VE Sbjct: 392 GHWVIDSYFRAGE---TALTDDGWFDTGDVATIDDDGYMIIRDRSKDIIKSGGEWISTVE 448 Query: 455 VESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMV 514 +E I SHP+I +AA +A W E P + G TE +++ + + K+ + + Sbjct: 449 LEDIAMSHPNIAQAAAIAAKHPKWDERPVVIAVKRSG---DVTEADLLAHYQGKVASWQI 505 Query: 515 PKTVVFKEELPKTSTGKVQKFILRD 539 P V+F E LP TGKVQK LR+ Sbjct: 506 PDRVIFVESLPLGGTGKVQKNTLRE 530 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: 766 Number of extensions: 50 Number of successful extensions: 7 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: 539 Length adjustment: 36 Effective length of query: 520 Effective length of database: 503 Effective search space: 261560 Effective search space used: 261560 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 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