Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_036258835.1 DL86_RS04845 malonyl-CoA synthase
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_000746085.1:WP_036258835.1 Length = 507 Score = 197 bits (502), Expect = 6e-55 Identities = 149/480 (31%), Positives = 226/480 (47%), Gaps = 16/480 (3%) Query: 50 YTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLL 109 ++Y + R +AL + LG++P DRV V +LGA++ G + + +N Sbjct: 30 FSYGDAVAASARSAAAL-SALGVKPGDRVAAQVEKSAAAVMLYLGAVRAGAIFLPLNPAY 88 Query: 110 TESDYEYMLTDSAARVAVVSQELLPLFAPMLGKV--PTLEHLVVAGGAGEDSLAALLATG 167 T ++ Y L+D+ V + + A ++ K P LE L G G S A L AT Sbjct: 89 TLAEIAYFLSDAEPAVVICDPDRRGELASLVAKAGAPLLETL---GADGRGSFADLCATQ 145 Query: 168 SEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSA 227 S F A PDD LY+SG+TG KG + H++L A DV+ A Sbjct: 146 SGDFSDAARGPDDLAAILYTSGTTGRSKGAMLTHANLASNAATLVEA-WRFTPADVLLHA 204 Query: 228 AKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLAN 287 ++ +GL + L + +A + Q GVPT Y +L Sbjct: 205 LPIYHTHGLFVAINTILFSAGRILFLARFDADECL---ALMPQASAMMGVPTFYTRLLRR 261 Query: 288 PDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHY 347 PD + +R S L + R W R G IL+ G TE I + G+ Sbjct: 262 PDVLRRASAHMRLFISGSAPLLAETHREWVERTGHAILERYGMTETNMIASNPYDGERIA 321 Query: 348 GTSGKPVPGYRLRLID-EDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGE-WT 405 GT G P+PG +R+ D E GA++ + G +++ GP+ YW NPEKTAA F + + Sbjct: 322 GTVGPPLPGVAVRIADPETGADLGRDKI-GVIEVKGPNVFKGYWRNPEKTAAEFRADGFF 380 Query: 406 RSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHL 465 +GD ++ GY GR+ D++ G V P EVE+ + A V+E+AVVG ED Sbjct: 381 ITGDLGKIDANGYVHIIGRAKDLIITGGFNVYPKEVEAEIDAIAGVVESAVVGLPHEDFG 440 Query: 466 IKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 A +V PG G EA +++ ++N LA +K P+ + FV++LP+ A GK+Q+ LR Sbjct: 441 EGIAAIVVRTPGSGLDEA---GVRSALENRLAKFKLPKRVIFVEELPRNAMGKVQKNALR 497 Lambda K H 0.319 0.138 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: 700 Number of extensions: 39 Number of successful extensions: 5 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: 527 Length of database: 507 Length adjustment: 35 Effective length of query: 492 Effective length of database: 472 Effective search space: 232224 Effective search space used: 232224 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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