Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_085124880.1 B9O00_RS21930 AMP-binding protein
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_900177295.1:WP_085124880.1 Length = 518 Score = 207 bits (526), Expect = 1e-57 Identities = 161/512 (31%), Positives = 245/512 (47%), Gaps = 22/512 (4%) Query: 27 DLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGI 86 +L+ R A +G + + D + TY +L R L LG+QP + V + + + + Sbjct: 12 ELLERQATA-QGERIAFRDARSAVTYADLEAVTGRLAGHL-ADLGVQPGESVAIFLPNSV 69 Query: 87 DFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVP-T 145 ++ + L ++ G V + I+ T + Y L D+ R V + E + L + G+VP Sbjct: 70 EWVESCLAVVRAGGVAVPISYDATAGEVAYRLADAGCRAVVTTDERVALLDGLRGEVPEA 129 Query: 146 LEHLVVAGGA-------GEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTV 198 + ++V G G A L A P D F LY+SG+TG KG + Sbjct: 130 IAPILVERGPERAAETPGGLRFAELAAREPASAPRDPRDIDVPAFILYTSGTTGRAKGVL 189 Query: 199 -HIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERP 257 +H L TA +A P+ G+ D V S LF +Y L ++ LAVGA+ LM + Sbjct: 190 LTVHGMLWVTAACWA-PLAGLARDDTVLSPLPLFHSYALNLSVLSILAVGASEYLMEKYS 248 Query: 258 TPAAVFERLRRHQPDIFYGVPTLYASML-ANPDCPKEGELRLRACTSAGEALPEDVGRRW 316 T AV L+ F GVPT++ L A P LR C SAG +P + R + Sbjct: 249 TGEAV-RLLQSGAYSFFPGVPTMFHYFLQATQQQPGLRFPALRVCVSAGAIMPATLNREF 307 Query: 317 QARFGVDILDGIGSTEMLHIFLSNRAGDVHY-GTSGKPVPGYRLRLIDE-DGAEITTAGV 374 + RFGV +LDG G TE + N G G+ G +PG +R++D GAE+ AG Sbjct: 308 EERFGVPLLDGYGITETSTMVTMNPLGAERVPGSCGPALPGLEVRIVDPLSGAEVP-AGA 366 Query: 375 AGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGI 434 GEL + GP+ + Y + P +TAA W +GD + G+ GR +++ G Sbjct: 367 EGELIVRGPNVMLGYHDKPAETAAALRDGWYHTGDLAKRDAAGFITITGRLKELIIRGGQ 426 Query: 435 YVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAG-EALRTDLKAHVK 493 ++P E+E + E VL+ AVVG E P F+V +P EA L AH + Sbjct: 427 NIAPAEIEEVVNLWEEVLDCAVVGMAHEHLGEVPALFVVAQPERAVDVEA----LLAHCR 482 Query: 494 NLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 L+ YK P + V+++P+T +GKI RF+L+ Sbjct: 483 TYLSAYKVPALVRLVEEIPRTGSGKIIRFRLK 514 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: 699 Number of extensions: 38 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: 518 Length adjustment: 35 Effective length of query: 492 Effective length of database: 483 Effective search space: 237636 Effective search space used: 237636 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