Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_012755263.1 RLEG_RS23870 AMP-binding protein
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_000023185.1:WP_012755263.1 Length = 528 Score = 179 bits (454), Expect = 2e-49 Identities = 147/484 (30%), Positives = 222/484 (45%), Gaps = 22/484 (4%) Query: 51 TYDELALRVNRCGSALRTTLGLQPKD-RVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLL 109 +Y EL R+ RC L LG + RV + + +D + G + + +N L Sbjct: 45 SYAELDTRIARCAGLLSDVLGARRDGGRVALLARNSLDSIVLAFACQRAGAIYVPLNWRL 104 Query: 110 TESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSE 169 ++ +L D A + V +E A + G P + + A G A A Sbjct: 105 NAAELRPILADCAPVLLVHDEEFAATVASLAGADPEMAVISTADGP-----AGFAARIEA 159 Query: 170 QFEAAPTRPDDH--CFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILG-IREGDVVFS 226 AAP D C LY+SG+TG PKG V + A ++ ++G I G V Sbjct: 160 SLPAAPVSADADGACVLLYTSGTTGQPKGVVITRRNAFFAAFNFS--VVGEIGPGSVALC 217 Query: 227 AAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDI--FYGVPTLYASM 284 F GL L +G T V+ ++R TPA L Q + ++ VP + ++ Sbjct: 218 DLPFFHTIGLIAVARTTLMLGGTLVV-SDRFTPARTLAALADRQRAVTHYFAVPQIALAL 276 Query: 285 LANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTE---MLHIFLSNR 341 +P L A G L + + + GV +++G G +E +LH+ + R Sbjct: 277 RNDPVYSAAALAGLHALFVGGAPLTQALIESYLDD-GVALVNGYGMSEAGTVLHVPIDRR 335 Query: 342 AGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFM 401 A + G+ G P P +R++ EDG E+ G GEL + GP+ YWN P++TAA F Sbjct: 336 AVQDNPGSVGLPAPLLDIRIVGEDGREVDD-GETGELWLRGPAVTPGYWNKPQETAAAFT 394 Query: 402 GEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWED 461 W R+GD G+Y R DM G V P EVE+AL +H A+L+AAVVG D Sbjct: 395 EGWYRTGDLGRREANGFYHIVDRLKDMYISGGENVYPAEVEAALASHPAILDAAVVGIPD 454 Query: 462 EDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQR 521 A++VL+PG A ++ H LA +K P I FV+ +P+TA+GK+Q+ Sbjct: 455 IRWGECGLAYVVLRPG---AVATGDEIAGHCAARLAAFKRPARILFVEAIPRTASGKVQK 511 Query: 522 FKLR 525 + LR Sbjct: 512 YVLR 515 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: 712 Number of extensions: 34 Number of successful extensions: 4 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: 528 Length adjustment: 35 Effective length of query: 492 Effective length of database: 493 Effective search space: 242556 Effective search space used: 242556 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