Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate PfGW456L13_2980 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2980 Length = 554 Score = 191 bits (484), Expect = 8e-53 Identities = 158/492 (32%), Positives = 236/492 (47%), Gaps = 15/492 (3%) Query: 45 DDAG-SYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPI 103 D AG SYT+ +L + R + L G++ D+V + I+ T + G V Sbjct: 52 DGAGASYTFTDLQDKAARFANYLLAQ-GVKKGDKVAGLLPRNIELLITVFATWRIGAVYQ 110 Query: 104 AINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAG----EDS 159 + T E+ L S A+V V P A + PT+ + A G G + S Sbjct: 111 PLFTAFGPKAIEHRLGSSGAKVVVTDAVNRPKLAEV-ADCPTIVTVTGAKGQGLVHGDFS 169 Query: 160 LAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIR 219 A LA S E +D +++SG+TG P + + I + Y R + +R Sbjct: 170 FWAELANYSAACEPVLLTGEDPFLLMFTSGTTG-PSKALSVPLKAIVAFQSYTRDAVDLR 228 Query: 220 EGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPT 279 D ++ A +AYG+ G+ P+++G T + + ++ G PT Sbjct: 229 PEDAFWNVADPGWAYGIYFGVTGPMSMGHPITFYDGPFTLESTCRVINKYGITNLTGSPT 288 Query: 280 LYASMLANPD-CPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFL 338 Y ++A D + + +LR +SAGE L +V R + V I D G TE L + L Sbjct: 289 AYRLLIAGGDEFARSIKGKLRIVSSAGEPLNPEVIRWFADNLDVVIHDHYGQTE-LGMVL 347 Query: 339 SNRAG---DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEK 395 N G +H G +G PG+R+ ++D++ E+ G G L I S + ++ E Sbjct: 348 CNHHGLEHPIHMGAAGFASPGHRIVVLDDEYKELGV-GQPGILAIDRSQSPMCWFAGYEG 406 Query: 396 -TAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEA 454 F+G + SGD N +G + GRSDD++ SG V P +VESALI H AV+EA Sbjct: 407 GPTKAFVGNYYLSGDTVEWNPDGSISFVGRSDDVITTSGYRVGPFDVESALIEHPAVVEA 466 Query: 455 AVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKT 514 AVVG D + KAF+VL P Y A L +L+ HV+ LA + YPR IEFV +LPKT Sbjct: 467 AVVGKPDPERTELVKAFVVLSPQYRAASELAEELRQHVRKRLAAHSYPREIEFVSELPKT 526 Query: 515 ATGKIQRFKLRS 526 +GK+QRF LR+ Sbjct: 527 PSGKLQRFILRN 538 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: 799 Number of extensions: 35 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: 554 Length adjustment: 35 Effective length of query: 492 Effective length of database: 519 Effective search space: 255348 Effective search space used: 255348 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