Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate AZOBR_RS21705 AZOBR_RS21705 2-aminobenzoate-CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__azobra:AZOBR_RS21705 Length = 545 Score = 280 bits (717), Expect = 7e-80 Identities = 185/525 (35%), Positives = 269/525 (51%), Gaps = 18/525 (3%) Query: 8 DHSNTPPAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALR 67 D S P + PER NAA L+ G + I + ++Y V+R L Sbjct: 23 DFSYDRPELTYPERLNAAAALLDVWRERGWDERPCVIGNDDVWSYGRFRDTVDRIARLLT 82 Query: 68 TTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAV 127 G+ P +RVLV + +L +K G V + LL ++ E ++ +A +A+ Sbjct: 83 ERFGIVPGNRVLVRGTNTPMLAACWLAVLKAGAVVVPTMPLLRATELESIIERAAVSLAL 142 Query: 128 V----SQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCF 183 +++L M G +P VV G+ L L F T DD Sbjct: 143 CDARFAKDLNGAAESMGGGMP-----VVTFNGGD--LEGWLEETEAGFAVVDTAADDVAL 195 Query: 184 WLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFP 243 ++SG+TG PK T H H DL+ A+L + +L DV L FAYG G L+FP Sbjct: 196 IAFTSGTTGKPKATAHFHRDLLAVADLSPQSLLRTGGDDVFCGTPSLAFAYGQGGMLLFP 255 Query: 244 LAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPD---CPKEGELRLRA 300 L VGA+ VL+ +R TP + E +H+ + + VPT+Y +M A + EG LRA Sbjct: 256 LRVGASVVLL-DRATPERLLEVTAKHKATVMFTVPTVYRAMTARIEEDASLAEGLRTLRA 314 Query: 301 CTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLR 360 C SAGE LP WQA G++ILD G+TEML+ L + G V G +G VPGY R Sbjct: 315 CVSAGEPLPATTLEGWQAVTGMEILDSFGTTEMLNAVLHSPPGAVRPGATGMVVPGYEAR 374 Query: 361 LIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYV 420 ++D D G G L + GP+ + Y ++P + G W +GD + ++++GY+ Sbjct: 375 VVD-DSLTPLPPGQIGRLAVRGPTGCI-YLDDPRQENYV-QGGWNLTGDAFRMDEDGYFW 431 Query: 421 YAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGA 480 Y R+DD++ +G +S +EVE L+ HEAV E AV+ D PKAFIV + G Sbjct: 432 YHARTDDLIVSAGYKISGLEVEDVLLGHEAVEECAVIAAPDPLRGSIPKAFIVTRDGVRP 491 Query: 481 GEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 + L L+ +VK+ +APYKYPR +EF++ LP+T TGKIQR+KLR Sbjct: 492 SDDLAERLQCYVKDRIAPYKYPRAVEFLEQLPRTETGKIQRYKLR 536 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: 784 Number of extensions: 42 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: 545 Length adjustment: 35 Effective length of query: 492 Effective length of database: 510 Effective search space: 250920 Effective search space used: 250920 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