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_015949835.1 G491_RS0127745 long-chain-fatty-acid--CoA ligase
Query= SwissProt::M4IQQ5 (556 letters) >NCBI__GCF_000429905.1:WP_015949835.1 Length = 555 Score = 246 bits (628), Expect = 2e-69 Identities = 187/564 (33%), Positives = 279/564 (49%), Gaps = 28/564 (4%) Query: 1 MEDLKPRPASSS---PLTPLGFLERAATVYG--DCTSVVYDA--VSYTWSQTHRRCLCLA 53 ME +K PA+S PL ++ + YG + S D YT+S + R LA Sbjct: 1 MELIKGFPATSQDRYPLNVTNIIKHSVRNYGPQEIASRRLDGSMFRYTYSDAYERMQRLA 60 Query: 54 SSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESK 113 + + LG++ G V VLA N + YE++F VP GA++ +NLRL + ++ ++ HS + Sbjct: 61 NGLTKLGVKVGDRVGVLAWNSNENYEVYFGVPGMGAVMLLLNLRLTPQDLAYVVEHSGCE 120 Query: 114 LIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDP 173 I VD L+ A AL P + V + + + E E SY++L+ DP Sbjct: 121 YIIVDET---LLPIAHALAPLCPQIKGYVVITMPGKKMSDVETPLENTHSYEELLAESDP 177 Query: 174 DFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLP 233 F W M + E YT+GTT PKGV + HR +++ ++ ++ G+ + +P Sbjct: 178 VFDWPMME-ETSAYAACYTTGTTGKPKGVYYSHRDVYLHSMCIGMNTGMNVKDTCCQIVP 236 Query: 234 MFHANGWSYPWGMAAVGGTNICLRKFDSEIIYDMIKR---HGVTHMCGAPVV----LNML 286 MFHA GW P VG I + E + + K GVT GAP + L + Sbjct: 237 MFHALGWGLPQAATLVGSRIILPGMYTLETLDSLSKLIVDEGVTMSAGAPAIFMPLLEYI 296 Query: 287 SNAPGSEPLKTTVQIMTAGAPPPSAVLFRT-ESLGFAVSHGYGLTETAGLVVS---CAWK 342 N P T V++++ PP +++ + G + H YG TET LV W Sbjct: 297 RNLE-ERPDLTGVRLLSGATEPPVSMMKGFWDMTGAEIIHAYGATETTPLVTINRLMPWL 355 Query: 343 KEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGY 402 + L ER LK +QG V + VVD T V DG T GE+++RG + Y Sbjct: 356 E--TSLSEDERWNLKKKQGFA-VGGLDVKVVD-ATLKDVAHDGKTPGEILIRGPWITGAY 411 Query: 403 LKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSH 462 P G+ S T DG++ +GDVG M +GYL+I DR KDVI SGGE +SSV++E+ + SH Sbjct: 412 HNAP-GSEASFTEDGFWRSGDVGTMDENGYLKITDRVKDVIKSGGEWISSVDMENEIISH 470 Query: 463 PDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKE 522 D+L+AAVV W E P A V L+ K +I + + ++ +P V+F + Sbjct: 471 NDVLDAAVVGVEHPKWQERPLALVVLRDDAKGKVNADDIRAHLSNVFAKWQLPDEVLFVD 530 Query: 523 ELPKTSTGKVQKFILRDMARGMGS 546 E+PKTS GK K ++R + M S Sbjct: 531 EIPKTSVGKTDKKVIRAEHKDMYS 554 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: 774 Number of extensions: 42 Number of successful extensions: 6 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: 555 Length adjustment: 36 Effective length of query: 520 Effective length of database: 519 Effective search space: 269880 Effective search space used: 269880 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