Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate PfGW456L13_1963 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1963 Length = 651 Score = 123 bits (308), Expect = 2e-32 Identities = 112/365 (30%), Positives = 167/365 (45%), Gaps = 22/365 (6%) Query: 179 DDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGN 238 ++ F LY+SGSTG PKG H + A + + R G++ + A + + G Sbjct: 256 EEALFILYTSGSTGKPKGVQHTTGGYLLYAAMTHERVFDYRPGEIYWCTADVGWVTGHSY 315 Query: 239 GLIFPLAVGATAVL---MAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGE 295 + PLA GAT +L + P V + + +H+ +I Y PT +M+A+ EG Sbjct: 316 IVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTAIRAMMASGTAAVEGA 375 Query: 296 --LRLRACTSAGEALPEDVGRRWQARFGVD---ILDGIGSTEMLHIFLSNRAGD--VHYG 348 LR S GE + + + G I+D TE +S G + G Sbjct: 376 DGSSLRLLGSVGEPINPEAWDWYYKNVGKSRCPIVDTWWQTETGGNMMSPLPGAHALKPG 435 Query: 349 TSGKPVPGYRLRLIDEDGAEITTAGVAGELQI--SGPSSAVMYWNNPEKTAATFMGEWTR 406 ++ +P G L+D G I G L I S P A + + ++ T+ + Sbjct: 436 SAARPFFGVVPALVDNLG-NIVEGEAEGNLVILDSWPGQARTLFGDHDRFVDTYFKTFRG 494 Query: 407 ---SGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDED 463 +GD + +GYY GR DD+L VSG + E+ESA++AH V EAAVVG Sbjct: 495 MYFTGDGARRDADGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVG---VP 551 Query: 464 HLIKPK---AFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQ 520 H IK + ++ LK G E LR +LK V+ + P P I++ LPKT +GKI Sbjct: 552 HDIKGQGIYVYVTLKNGEEPNEQLRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIM 611 Query: 521 RFKLR 525 R LR Sbjct: 612 RRILR 616 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: 922 Number of extensions: 57 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: 651 Length adjustment: 37 Effective length of query: 490 Effective length of database: 614 Effective search space: 300860 Effective search space used: 300860 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