Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate BWI76_RS17800 BWI76_RS17800 long-chain-fatty-acid--CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Koxy:BWI76_RS17800 Length = 572 Score = 176 bits (446), Expect = 2e-48 Identities = 155/550 (28%), Positives = 240/550 (43%), Gaps = 51/550 (9%) Query: 14 PAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQ 73 PA P+RY + +L + + + +I+ TY +L R + L+ LGLQ Sbjct: 25 PAEINPDRYQSLVELF-EHAVRRYADQPAFINMGEVMTYRKLEERSRAFAAYLQEGLGLQ 83 Query: 74 PKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDS-AARVAVVSQEL 132 DRV + + + + +P G ++ G++ + +N L T + E+ L DS AA + +VS Sbjct: 84 KGDRVALMMPNLLQYPVALFGILRAGMIVVNVNPLYTPRELEHQLNDSGAAAIVIVSN-- 141 Query: 133 LPLFAPMLGKV---PTLEHLVVAGGAGEDSLA---------------------------- 161 FA L KV ++H+++ + S A Sbjct: 142 ---FAHTLEKVVDKTQVKHVILTRMGDQLSPAKGTVVNFVVKYIKRLVPKYHLPDAISFR 198 Query: 162 -ALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYAR---PILG 217 AL Q+ P D F Y+ G+TG KG + H +++ E P+L Sbjct: 199 SALQHGYRMQYIKPEIVPQDLAFLQYTGGTTGVAKGAMLTHRNMLANLEQVNGTYGPLLH 258 Query: 218 IREGDVVFSAAKLFFAYGLG-NGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYG 276 R ++V +A L+ + L N L+F G ++ R P V E L ++ G Sbjct: 259 -RGKELVVTALPLYHIFALTMNCLLFIELGGQNLLITNPRDIPGLVKE-LAKYPFTAMTG 316 Query: 277 VPTLYASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHI 336 V TL+ ++L N + + L G + + V RW G +L+G G TE + Sbjct: 317 VNTLFNALLNNKEFQQLDFSSLHLSAGGGMPVQQVVAERWVKLTGQYLLEGYGLTECAPL 376 Query: 337 FLSNRAG-DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEK 395 N D H G+ G PVP +L+D+D E+ G GEL + GP + YW P+ Sbjct: 377 VSVNPHDIDYHSGSIGLPVPSTEAKLVDDDDNEVPP-GEPGELCVKGPQVMLGYWQRPDA 435 Query: 396 TAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAA 455 TA W +GD ++++EG+ R DM+ VSG V P E+E ++ H V E A Sbjct: 436 TAEIIKDGWLHTGDIAVMDEEGFLRIVDRKKDMILVSGFNVYPNEIEDVVMQHAGVQEVA 495 Query: 456 VVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTA 515 VG K F+V K E L T + L YK P+ +EF D+LPK+ Sbjct: 496 AVGVPSGSSGEAVKIFVVKKDPTLTEEMLIT----FCRRQLTGYKVPKHVEFRDELPKSN 551 Query: 516 TGKIQRFKLR 525 GKI R +LR Sbjct: 552 VGKILRRELR 561 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: 694 Number of extensions: 45 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: 572 Length adjustment: 36 Effective length of query: 491 Effective length of database: 536 Effective search space: 263176 Effective search space used: 263176 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: 53 (25.0 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