Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_011426974.1 RHE_RS19290 AMP-binding protein
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_000092045.1:WP_011426974.1 Length = 550 Score = 206 bits (523), Expect = 2e-57 Identities = 161/524 (30%), Positives = 252/524 (48%), Gaps = 22/524 (4%) Query: 17 KIPERYNAADDLIGRNLL---AGRGGKTVYID------DAGSYTYDELALRVNRCGSALR 67 +IPE +N IGR + A R + V ++ D S TY EL+ + +AL Sbjct: 19 RIPEDFN-----IGRAVSDEWAARDPERVCLEHFSPNGDHLSLTYGELSAASSMFANAL- 72 Query: 68 TTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAV 127 +LG++ DRV + V + + K G + + + L EY L S A + Sbjct: 73 ASLGIKRGDRVALLVPQSFETVIAHVAIYKIGAIALPLALLFGVEALEYRLRISGAAAII 132 Query: 128 VSQELLPLFAPMLGKVPTLEHLV-VAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFWLY 186 + L + ++P L H++ V+ A S A L+A+ + FE T PDD ++ Sbjct: 133 TNDFGLDRVRQIRDRLPELRHVISVSDAADALSFADLIASHASVFEGEKTTPDDAALMIF 192 Query: 187 SSGSTGAPKGTVHIHSDLI-HTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLA 245 +SG+TG PKG +H H L H + + GD V++ + +A GL N L+ L Sbjct: 193 TSGTTGPPKGALHGHRVLPGHIPGMQFAHEGFPKVGDKVWTPSDWAWAGGLLNALLPSLL 252 Query: 246 VGATAVLM-AERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSA 304 +G V A++ + + + + PT M + D + +L LR SA Sbjct: 253 LGVPVVSSPAQKFDADTAYRIMAEMKVRNAFIPPTALRLMRSVSDPRSKYDLVLRTVGSA 312 Query: 305 GEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRA-GDVHYGTSGKPVPGYRLRLID 363 GEAL + + G+ + + G TE + S+ A G G G+ VPG+R+ ++ Sbjct: 313 GEALGRETYDWARRTLGITVNEFYGQTECNFVLSSSAAFGVTKAGAIGRAVPGHRVAIVS 372 Query: 364 EDGAEITTAGVAGELQISGPSSAVM--YWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVY 421 E G E+ AG +G++ I+ P + YWN+ T F+ W +GD +++GY + Sbjct: 373 EAGDELP-AGESGQIAIASPDPVMFLGYWNDAAATERKFLHGWLLTGDIGRQDEDGYVTF 431 Query: 422 AGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAG 481 GR DD++ SG + P E+E L H AV AA VG D KA+IVL PG+ Sbjct: 432 EGRDDDVITSSGYRIGPAEIEDCLTGHPAVQLAAAVGKPDVVRTEIVKAYIVLSPGHSPS 491 Query: 482 EALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 EAL +++ VK L+ ++YPR +EFV+ LP T TGK+ R LR Sbjct: 492 EALAAEIREWVKMRLSMHEYPREVEFVESLPLTTTGKVIRRLLR 535 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: 717 Number of extensions: 36 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: 550 Length adjustment: 35 Effective length of query: 492 Effective length of database: 515 Effective search space: 253380 Effective search space used: 253380 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 Apr 09 2024. 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