Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate GFF2312 PGA1_c23440 putative benzoate-CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Phaeo:GFF2312 Length = 538 Score = 285 bits (728), Expect = 4e-81 Identities = 186/512 (36%), Positives = 265/512 (51%), Gaps = 11/512 (2%) Query: 19 PERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRV 78 PER NAA +L + G G T I + TY EL NR L LG+QP +R+ Sbjct: 33 PERLNAAVELTDAMVAKGFGDHTALIGNGRRRTYKELTDWTNRLAHVLVEDLGVQPGNRI 92 Query: 79 LVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAP 138 L+ + +L A K G V + +L + ++ + A+ L+ Sbjct: 93 LIRSANNPAMVACWLAATKAGAVVVNTMPMLRAGELAKIIDKAEISHALCDTRLMEELVA 152 Query: 139 MLGKVPTLEHLVVAGGAG--EDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKG 196 L+ +V G + L L +FEA T DD ++SG+TG+PK Sbjct: 153 CAKTSAHLKSVVGFDGTSNHDAELDRLALEKPVRFEAVATGRDDVALLGFTSGTTGSPKA 212 Query: 197 TVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAER 256 T+H H DL+ A+ YA +L + D+ + L F +GLG IFPL GA A L+ E Sbjct: 213 TMHFHRDLLMIADGYAAEVLQVTPEDIFVGSPPLAFTFGLGGLAIFPLRFGAAATLL-EN 271 Query: 257 PTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGE--LRLRACTSAGEALPEDVGR 314 +P + E + ++ + + PT Y ML +EG LRA SAGE LP V Sbjct: 272 ASPPNLIEIIETYKATVCFTAPTAYRVMLR---AMEEGADLSSLRAAVSAGETLPAPVYD 328 Query: 315 RWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGV 374 W A+ G +LDGIG+TEMLHIF+SNR D +GKPV GYR+R++D DG E G Sbjct: 329 EWIAQTGKPMLDGIGATEMLHIFISNRFDDHRPACTGKPVKGYRVRVLDSDGNE-APRGE 387 Query: 375 AGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGI 434 G L + GP+ Y + + G W +GD ++++ +GY +A R+DDM+ +G Sbjct: 388 VGRLAVKGPTGC-RYLADARQGEYVKDG-WNITGDSFVMDVDGYLHFAARNDDMIVSAGY 445 Query: 435 YVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKN 494 ++ EVE+AL++H+ V E AV+G D+ +A +VL G A E L L+ HVK Sbjct: 446 NIAGPEVEAALLSHDLVTECAVIGASDDARGEIVQAHVVLAEGAQASEVLTRALQDHVKA 505 Query: 495 LLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 +APYKYPR I + D LPKT TGKIQRF+L+S Sbjct: 506 AIAPYKYPRDIVYTDALPKTETGKIQRFRLKS 537 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: 766 Number of extensions: 35 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: 538 Length adjustment: 35 Effective length of query: 492 Effective length of database: 503 Effective search space: 247476 Effective search space used: 247476 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