Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate HSERO_RS04625 HSERO_RS04625 AMP-binding protein
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__HerbieS:HSERO_RS04625 Length = 556 Score = 186 bits (473), Expect = 1e-51 Identities = 154/485 (31%), Positives = 236/485 (48%), Gaps = 15/485 (3%) Query: 50 YTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLL 109 Y++ ++ R + LR G+QP V + + T LG ++ G V + T Sbjct: 67 YSFAQVRSMAARVANLLRQQ-GIQPGQIVAGMLPRTPELLATVLGTLRAGAVYQPLFTAF 125 Query: 110 TESDYEYMLTDSAARVAVVS---QELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLAT 166 E+ L S A + V + ++ L A +V T+ AG+ A + Sbjct: 126 GPKAIEHRLALSGASLIVTNVANRDKLDEIANC-PQVCTVRESNDPLRAGDIDFRAAVDA 184 Query: 167 GSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFS 226 S+ F D + +SG+TGA KG V + + +Y R +G+ D ++ Sbjct: 185 QSDDFAPVLRSGADLMLMMSTSGTTGAAKG-VPVPLSALQAFSVYMREAVGLLPQDKFWN 243 Query: 227 AAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLA 286 A +AYGL +I PLA+G T + +E +RR G PT Y M+A Sbjct: 244 MADPGWAYGLYYAIIGPLAIGHGITFNEAAFTVSGTYETIRRLGITSLAGAPTAYRMMMA 303 Query: 287 -NPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRA--G 343 + + RLRA +SAGE L +V R + + V I D G TE+ + ++ A Sbjct: 304 AGEEAAASVKGRLRAVSSAGEPLNAEVVRWFASALDVPIHDHYGQTELGMVVNNHHALRH 363 Query: 344 DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNN---PEKTAATF 400 +V G++G +PGYR+ ++DE+ E+ A GEL I S +YW + + T A Sbjct: 364 EVVPGSAGFAMPGYRVVVLDENHQELG-ANQPGELAIDIARSP-LYWFSGYWKQDTPAIA 421 Query: 401 MGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWE 460 G ++ +GD + G + GRSDD++ +G + P +VESAL+ H AV + AV+G Sbjct: 422 HGYYS-TGDNVELEPNGSISFIGRSDDVITSAGYRIGPFDVESALLEHPAVADVAVIGLP 480 Query: 461 DEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQ 520 D + KAF+VL + A +ALR L HVK L+ + YPR IEF+D LPKT +GK+Q Sbjct: 481 DPERTEIVKAFVVLSDQFKASDALREQLAQHVKRRLSAHAYPRAIEFLDALPKTPSGKLQ 540 Query: 521 RFKLR 525 RF LR Sbjct: 541 RFVLR 545 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: 705 Number of extensions: 38 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: 556 Length adjustment: 35 Effective length of query: 492 Effective length of database: 521 Effective search space: 256332 Effective search space used: 256332 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