Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate GFF1013 PGA1_c10300 acetyl-coenzyme A synthetase AcsA
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Phaeo:GFF1013 Length = 516 Score = 164 bits (416), Expect = 6e-45 Identities = 140/463 (30%), Positives = 223/463 (48%), Gaps = 33/463 (7%) Query: 72 LQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQE 131 +QP DRV V + +D L K G + + + L A+R+ E Sbjct: 72 VQPGDRVGVLLSQSVDCAVAHLAIWKIGAISVPLFKLFQHDAL-------ASRIGDAGLE 124 Query: 132 LLPLFAPMLGKVPTL-EHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGS 190 L+ ++ +L + L+VA D L+A A T P+ +Y+SG+ Sbjct: 125 LVLTDGGGTAQLGSLAQPLLVA-----DILSASTGQSDHLLPYAETTPETPAVLIYTSGT 179 Query: 191 TGAPKGTVHIHSDLIH--TAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGA 248 TG+ KG +H H L + LG + GD +++ A + GL + L+ LA+G Sbjct: 180 TGSAKGALHGHRVLSGHLPGVAISHDHLG-QPGDCLWTPADWAWIGGLFDVLMPGLALGV 238 Query: 249 TAVLMA-ERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEA 307 V ++ TP A E +R+ + PT + A +G LR+ S GE Sbjct: 239 PVVAARLDKFTPEACAEIIRQGDVRNVFFPPTALRLLKA----AGQGLDGLRSVASGGEP 294 Query: 308 LPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGD--VHYGTSGKPVPGYRLRLIDED 365 L ++ Q GV I + G TE ++ +S+ D V G G+PVPG + ++D+ Sbjct: 295 LGAEMLAWGQRHLGVTINEFYGQTEC-NMTVSSCVADFPVRPGCIGRPVPGCTVEVLDDT 353 Query: 366 GAEITTAGVAGELQISGPSSAVM--YWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAG 423 G T G++ + ++++M YWN P+ TA F +W +GD+ + + Y + G Sbjct: 354 G---TPTKDEGDVAVRRGAASMMLEYWNRPDATAEKFHADWLITGDRGIWEGD-YLRFVG 409 Query: 424 RSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEA 483 R DD++ +G + P E+E L+ H AV VVG DE KA++VLKPG+ E Sbjct: 410 REDDVITSAGYRIGPAEIEDCLMTHPAVATVGVVGKPDELRTEIVKAYVVLKPGHSPSE- 468 Query: 484 LRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 +DL+ +VK+ LA Y YPR +EF+D LP T TGK+ R +L++ Sbjct: 469 --SDLQDYVKSRLAKYSYPREVEFLDALPMTVTGKVIRKELKA 509 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: 783 Number of extensions: 44 Number of successful extensions: 7 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: 516 Length adjustment: 35 Effective length of query: 492 Effective length of database: 481 Effective search space: 236652 Effective search space used: 236652 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