Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate H281DRAFT_01203 H281DRAFT_01203 acetyl-CoA synthetase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Burk376:H281DRAFT_01203 Length = 567 Score = 183 bits (465), Expect = 1e-50 Identities = 150/495 (30%), Positives = 232/495 (46%), Gaps = 24/495 (4%) Query: 44 IDDAGS----YTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGG 99 +DD S +Y +++ R R + LR+ +G++ DRVL+ + + ++ L A+K G Sbjct: 58 VDDPASEGLRLSYAQMSERSARMANFLRS-VGVKRGDRVLLMLPNRVELWDVMLAAMKLG 116 Query: 100 VVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDS 159 + + T L+ D + A VV L F + VP V AG Sbjct: 117 AIVLPATTQLSADDVRDRVQIGGANFVVVDSAELSKFDSL--DVPLTRLSVGTPRAGWTD 174 Query: 160 LAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSD--LIHTAELYARPILG 217 LAA + TR D ++SG+T PK H H + H + +Y +G Sbjct: 175 LAAAYDASPQFTPDGVTRAADPLLLYFTSGTTSKPKLVEHTHQSYPVGHLSTMYW---IG 231 Query: 218 IREGDVVFSAAKLFFAYGLGNGLIFPL-AVGATAVLMAERPTPAAVFERLRRHQPDIFYG 276 ++ GD+ ++ + +A + P A V R P + L R Sbjct: 232 LQPGDIHWNISSPGWAKHAWSCFFAPWNAQACVFVFNFARFVPKDTLDVLVRFNVTTVCA 291 Query: 277 VPTLYASMLAN--PDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEML 334 PT++ ++ D P ++LR AGE L ++ R + +G+ I DG G TE Sbjct: 292 PPTVWRMLVQEHLTDYP----VKLREIVGAGEPLNPEIIERVKHAWGITIRDGFGQTETT 347 Query: 335 HIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVM----YW 390 ++ V G+ G+P+PGYR+ L+D D +T +A + G + Y Sbjct: 348 CQIGNSPGQPVVAGSMGRPLPGYRIELLDADDQPVTEGEIALPIGPDGKQRPLGLMTGYA 407 Query: 391 NNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEA 450 N+ + TA + R+ D L ++GYYVY GR+DD+ K S +SP E+ES LI HEA Sbjct: 408 NSEQATAQAMRNGFYRTSDVALRREDGYYVYVGRADDVFKSSDYRLSPFELESVLIEHEA 467 Query: 451 VLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDD 510 + EAAVV D L PKAF+ ++ GY AG L + A + LAPYK R ++F + Sbjct: 468 IGEAAVVPSADALRLSVPKAFVTVRHGYQAGPELARAVFAFSREKLAPYKRIRRLQF-SE 526 Query: 511 LPKTATGKIQRFKLR 525 LPKT +GKI+R +LR Sbjct: 527 LPKTISGKIRRVELR 541 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: 715 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: 567 Length adjustment: 36 Effective length of query: 491 Effective length of database: 531 Effective search space: 260721 Effective search space used: 260721 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