Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate 3609616 Dshi_2999 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Dino:3609616 Length = 506 Score = 179 bits (453), Expect = 3e-49 Identities = 148/507 (29%), Positives = 225/507 (44%), Gaps = 25/507 (4%) Query: 26 DDLIGRNLLAGRGGKTVYIDDAGSYTYD---ELALRVNRCGSALRTTLGLQPKDRVLVCV 82 D L GRN AG + + + T+ ELA R +A T LGL P DR+ + V Sbjct: 7 DALFGRN--AGSDAPFLQLPGGDTLTHGGFVELAARY----AATLTGLGLAPGDRLALQV 60 Query: 83 LDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGK 142 + + G ++ G+V + +NT T ++ Y + +S A++ + P+ + Sbjct: 61 EKSPEALAVYAGCVQAGIVFLPLNTAYTPAEISYFVGNSGAKLVLCDPRAEAGLTPVAAE 120 Query: 143 VPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHS 202 + A G G AA AT FE DD +LY+SG+TG KG + Sbjct: 121 AGAQLLTLAADGTGSFPDAA--ATAPATFETVARTEDDLAAFLYTSGTTGRSKGAMLSQR 178 Query: 203 DLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAV 262 +L+ AE+ + DV+ A +F +GL G L G + + + + A + Sbjct: 179 NLLSNAEVLV-DYWRFTDKDVLLHALPIFHTHGLFVGTNITLLAGGSMIFLPKFDAEAVL 237 Query: 263 FERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGV 322 R GVPT Y +LA ++ +R S L + R ++AR G Sbjct: 238 ANLPRA---TTMMGVPTFYTRLLAEDRFDRDLVAHMRLFVSGSAPLLAETHREFEARTGH 294 Query: 323 DILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISG 382 IL+ G TE + G GT G P+PG L++ D D G G++++ G Sbjct: 295 RILERYGMTETNMNTSNPYDGARRAGTVGFPLPGVELKVCDPDTGAELPQGEIGQIEVRG 354 Query: 383 PSSAVMYWNNPEKTAATFMGE-WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEV 441 P+ YW PEKTAA + + +GD L++D+GY GR D++ G + P EV Sbjct: 355 PNVFQGYWQMPEKTAAELRADGFFITGDLGLIDDQGYVQIVGRGKDLIISGGYNIYPKEV 414 Query: 442 ESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNL---LAP 498 E AL VLE+AV+G D +V +PG R D +A L LA Sbjct: 415 ELALDEAPGVLESAVIGAPHPDFGESVVGILVPQPG------ARIDTEAVAARLAGQLAR 468 Query: 499 YKYPRWIEFVDDLPKTATGKIQRFKLR 525 +K PR + +D LP+ GK+Q+ LR Sbjct: 469 FKQPRKLVVMDALPRNTMGKVQKNVLR 495 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: 47 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: 527 Length of database: 506 Length adjustment: 35 Effective length of query: 492 Effective length of database: 471 Effective search space: 231732 Effective search space used: 231732 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 Sep 17 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