Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate Ac3H11_4556 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4556 Length = 553 Score = 280 bits (716), Expect = 1e-79 Identities = 174/513 (33%), Positives = 258/513 (50%), Gaps = 6/513 (1%) Query: 14 PAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQ 73 P ++I ++ N L + AG + + +YTY + R L GL Sbjct: 30 PELQIADQANLVQALFDQAERAGHSDRPLLRGPHRTYTYRDARTEAARIAEVLTQDHGLV 89 Query: 74 PKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELL 133 P +RVL+ + ++ +LG + G+V +A LL + ++ + +A+ LL Sbjct: 90 PGNRVLLRGGNTVEMALAWLGTVYAGLVAVATMPLLRAVELGSIIDRAQPTLALCDGRLL 149 Query: 134 PLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSE-QFEAAPTRPDDHCFWLYSSGSTG 192 + P L +V A + + A G PT DD ++SG+TG Sbjct: 150 AELQAAQTQHPVLTTIVPFHTAPDAADLLQRAQGKPGTTPPCPTSADDIALMAFTSGTTG 209 Query: 193 APKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVL 252 APK VH H D++ E + R +L D+V + L F +GLG L+FP+ GA+ Sbjct: 210 APKAAVHTHRDVLAGCEAWPRHVLKATPDDIVAGSPPLAFTFGLGGLLVFPMWAGASVYF 269 Query: 253 MAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPEDV 312 + TP + +R I Y PT Y M P + G +LR SAGE LP+ Sbjct: 270 PDQPYTPETMVRLMREAGVTICYTAPTFYRQMA--PFARQIGLPQLRTSVSAGEGLPDAT 327 Query: 313 GRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTA 372 + W+ G+D+ DGIG+TEM HIF+S+ G+ G GK VPGY +++D+DG E+ Sbjct: 328 RQLWREATGLDMTDGIGATEMFHIFISSAGGESRAGAVGKVVPGYTAKVVDDDGHEVPR- 386 Query: 373 GVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVS 432 G G+L + GP+ Y ++P + G W GD + + +GY+ Y R DDM+ + Sbjct: 387 GTVGKLAVIGPTGC-KYLDDPRQAKYVKDG-WNYPGDAFTQDADGYFFYQARDDDMIITA 444 Query: 433 GIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHV 492 G V EVE AL+ H AV E V+G DE+ + KA VLKPG+ A+ L+ HV Sbjct: 445 GYNVGGPEVEDALLRHPAVAECGVIGVPDEERGMVVKAICVLKPGHTGDAAMVKTLQDHV 504 Query: 493 KNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 K +AP+KYPR +EFV LP+T TGK+QRFKLR Sbjct: 505 KATIAPFKYPRVVEFVAALPRTETGKLQRFKLR 537 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: 830 Number of extensions: 46 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: 553 Length adjustment: 35 Effective length of query: 492 Effective length of database: 518 Effective search space: 254856 Effective search space used: 254856 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