Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_072781751.1 BUA36_RS04545 fatty-acid--CoA ligase
Query= metacyc::MONOMER-20124 (573 letters) >NCBI__GCF_900143065.1:WP_072781751.1 Length = 543 Score = 184 bits (468), Expect = 6e-51 Identities = 153/508 (30%), Positives = 249/508 (49%), Gaps = 22/508 (4%) Query: 67 RYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIYELHFAVPMAGGILCTLNAR 126 RYT+ R +LA AL LG+ G+ VAT ++N E ++AV +G +L T+N R Sbjct: 40 RYTFRDCAQRAKQLAKALQA-LGLQMGERVATLAWNGYRHLEAYYAVSGSGAVLHTINPR 98 Query: 127 NDSAMVSTLLAHSEAKLIFVEPQLLETARAALDLLAQKDIKPPTLVLLTDSESFTSSSYD 186 ++ + H+E + + + L A K +K L+ D ++ + Sbjct: 99 LHPEQLAYICNHAEDQYLLFDFCFLPLVEAIAPHC--KTVKGFVLLGAADRMPAQTNIPN 156 Query: 187 H--YNHLLANGSDDFEIRRPKNEWDPISINYTSGTTARPKAVVYSHRGAYLNSIATVLLH 244 Y LLA S D+ +E ++ YTSGTT PK +YSHR L++ A+ L + Sbjct: 157 LLCYEDLLAAQSPDYTWPT-FDEHAAATLCYTSGTTGNPKGALYSHRSTVLHAYASALPN 215 Query: 245 GMGTTS--VYLWSVPMFHCNGWCFPWGAAAQGATNICIRK-VSPKAIFDNIHLHKVTHFG 301 + +S + VPMFH N W P+ GA + + K++++ + KVT Sbjct: 216 VLNVSSRDSVMPVVPMFHVNAWGLPYSVPLSGAKMVFPGPALDGKSVYELMEQEKVTFSA 275 Query: 302 AAPTV-LNMIVNSPEGNLHTPLPHKVEVMTGGSPPPPKVIARMEEMGFQVNHIYGLTETC 360 PTV L +I + + L H+ V+ G + PP + ++E QV H +G+TE Sbjct: 276 GVPTVWLGLINYAMQHQLKFSTFHRT-VIGGSACPPAMMNTLIDEFDVQVIHGWGMTEMS 334 Query: 361 --GPAANCVCKPEWDALQPEERYALKARQGLNHLAMEEMDVRDPVTMESVRADGATIGEV 418 G + K + + +R L+ +QG + + +M + D + E + DG T G + Sbjct: 335 PLGTTGGLLSK-HLELPKAAQRQILQ-KQG-HAIYGVDMKIVDELG-EELPWDGVTSGSL 390 Query: 419 MFRGNTVMSGYFKDLKATEEAFEGGWFRSGDLGVKHEDGYIQLKDRKKDVVISGGENIST 478 + +G +++ YFK + E GWF +GD+ DG++Q+ DR KDV+ SGGE I T Sbjct: 391 LVKGPWIIASYFKGEGG--DVLEDGWFPTGDVATIDADGFMQITDRAKDVIKSGGEWIGT 448 Query: 479 VEVETVLYSHEAVLEAAVVARPDKLWGETPCAFVTLKEGFDNDVSADQIIKFCRDRLPHY 538 +++E + SH AV++AA + W E P V K G +VS +Q++ ++ + Sbjct: 449 IDLENIAMSHPAVMQAACIGVFHPKWDERPLLVVVRKPG--QEVSREQLLAHFDGKVAKW 506 Query: 539 MAPKTVVF-EELPKTSTGKIQKYILKEK 565 P VVF + LP TGKIQK L+E+ Sbjct: 507 WLPDDVVFADALPVGGTGKIQKNKLREQ 534 Lambda K H 0.318 0.133 0.408 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: 777 Number of extensions: 52 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: 573 Length of database: 543 Length adjustment: 36 Effective length of query: 537 Effective length of database: 507 Effective search space: 272259 Effective search space used: 272259 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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