Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate 15923 b1805 acyl-CoA synthase (NCBI)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Keio:15923 Length = 561 Score = 174 bits (440), Expect = 1e-47 Identities = 143/541 (26%), Positives = 236/541 (43%), Gaps = 43/541 (7%) Query: 19 PERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRV 78 P+RY + D+ +++ A + +++ T+ +L R + L+ LGL+ DRV Sbjct: 19 PDRYQSLVDMFEQSV-ARYADQPAFVNMGEVMTFRKLEERSRAFAAYLQQGLGLKKGDRV 77 Query: 79 LVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAP 138 + + + + +P G ++ G++ + +N L T + E+ L DS A V+ Sbjct: 78 ALMMPNLLQYPVALFGILRAGMIVVNVNPLYTPRELEHQLNDSGASAIVIVSNFAHTLEK 137 Query: 139 MLGKVPTLEHLVVAGGAGEDSLA-----------------------------ALLATGSE 169 ++ K ++H+++ + S A AL Sbjct: 138 VVDKT-AVQHVILTRMGDQLSTAKGTVVNFVVKYIKRLVPKYHLPDAISFRSALHNGYRM 196 Query: 170 QFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYAR---PILGIREGDVVFS 226 Q+ P+D F Y+ G+TG KG + H +++ E P+L + ++V + Sbjct: 197 QYVKPELVPEDLAFLQYTGGTTGVAKGAMLTHRNMLANLEQVNATYGPLLHPGK-ELVVT 255 Query: 227 AAKLFFAYGLG-NGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASML 285 A L+ + L N L+F G ++ R P V E L ++ GV TL+ ++L Sbjct: 256 ALPLYHIFALTINCLLFIELGGQNLLITNPRDIPGLVKE-LAKYPFTAITGVNTLFNALL 314 Query: 286 ANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAG-D 344 N + + L G + + V RW G +L+G G TE + N D Sbjct: 315 NNKEFQQLDFSSLHLSAGGGMPVQQVVAERWVKLTGQYLLEGYGLTECAPLVSVNPYDID 374 Query: 345 VHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEW 404 H G+ G PVP +L+D+D E+ G GEL + GP + YW P+ T W Sbjct: 375 YHSGSIGLPVPSTEAKLVDDDDNEVPP-GQPGELCVKGPQVMLGYWQRPDATDEIIKNGW 433 Query: 405 TRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDH 464 +GD ++++EG+ R DM+ VSG V P E+E ++ H V E A VG Sbjct: 434 LHTGDIAVMDEEGFLRIVDRKKDMILVSGFNVYPNEIEDVVMQHPGVQEVAAVGVPSGSS 493 Query: 465 LIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKL 524 K F+V K E+L T + L YK P+ +EF D+LPK+ GKI R +L Sbjct: 494 GEAVKIFVVKKDPSLTEESLVT----FCRRQLTGYKVPKLVEFRDELPKSNVGKILRREL 549 Query: 525 R 525 R Sbjct: 550 R 550 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: 692 Number of extensions: 46 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 527 Length of database: 561 Length adjustment: 35 Effective length of query: 492 Effective length of database: 526 Effective search space: 258792 Effective search space used: 258792 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