Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_010442785.1 G7G_RS0117685 AMP-binding protein
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_000192475.1:WP_010442785.1 Length = 508 Score = 169 bits (427), Expect = 3e-46 Identities = 153/527 (29%), Positives = 243/527 (46%), Gaps = 62/527 (11%) Query: 18 IPERYNAADDLIGRNLLAGRGGKTVYID----DAGSYTYDELALRVNRCGSALRTTLGLQ 73 IP+R N A R L+ + +D D T+ +L V+ AL + + Sbjct: 18 IPDRLNMA-----RQCLSQPSEQVAILDLTASDPREVTFGDLGEMVDGIARALINDV--R 70 Query: 74 PKDRVLVCVLDGIDFPTTFLGAIKGGVVPI---------AINTLLTESDYEYMLTDSAAR 124 P DRV V + L K G + + A+++ + ++ +++LTDS Sbjct: 71 PGDRVGVLLSQSPGCAAAHLAIWKIGAISVPLFKLFKHDALSSRVGDAGLKFVLTDSEG- 129 Query: 125 VAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFW 184 A+V P+ A +G+ A T P++ Sbjct: 130 AALVGDLAKPVLADQIGQE------------------------GPPVPFADTSPEEPAVL 165 Query: 185 LYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPL 244 +Y+SG+TG+PKG +H H L + +R+GD +++ A + GL + L+ L Sbjct: 166 IYTSGTTGSPKGALHGHRVLTGHLPGVSISHNHLRQGDCLWTPADWAWIGGLFDVLMPGL 225 Query: 245 AVGATAVLMA-ERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTS 303 A+G V ++ TP A + + R + PT ML D G LR+ S Sbjct: 226 ALGVPIVAARLDKFTPEACADLVMRGGVRNVFFPPTALR-MLKAADQTIPG---LRSVAS 281 Query: 304 AGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGD--VHYGTSGKPVPGYRLRL 361 GE L ++ + FG+ I + G TE ++ +S+ A D H G GKPVPG+ + + Sbjct: 282 GGEPLGVEMLAWGKKAFGLTINEFYGQTEC-NMVVSSCAEDFPAHPGCIGKPVPGHEVAV 340 Query: 362 IDEDGAEITTAGVAGELQISGPSSAVM--YWNNPEKTAATFMGEWTRSGDKYLVNDEGYY 419 ID DG G ++ I S+++M YWN P+ T F G+W +GD+ + + Y Sbjct: 341 IDGDGRPTNEEG---DVAIRRGSASMMLEYWNRPDATTEKFRGDWLITGDRGVWEGD-YL 396 Query: 420 VYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYG 479 + GR DD++ +G + P E+E L+ H AV VVG D KA++VLKPG Sbjct: 397 RFVGRDDDVITSAGYRIGPAEIEDCLLTHPAVATVGVVGKPDPLRTEIVKAYVVLKPG-- 454 Query: 480 AGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 EA +L+ VK+ LA Y YPR + F+D+LP T TGK+ R +L++ Sbjct: 455 -AEAAEQELQDWVKDRLAQYSYPREVAFLDELPMTVTGKVIRKELKA 500 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: 702 Number of extensions: 47 Number of successful extensions: 6 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: 508 Length adjustment: 35 Effective length of query: 492 Effective length of database: 473 Effective search space: 232716 Effective search space used: 232716 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 24 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