Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate BPHYT_RS28035 BPHYT_RS28035 AMP-dependent synthetase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__BFirm:BPHYT_RS28035 Length = 563 Score = 176 bits (447), Expect = 2e-48 Identities = 146/480 (30%), Positives = 221/480 (46%), Gaps = 16/480 (3%) Query: 51 TYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLT 110 +Y +++ R R + LR +G+ DR+L+ + + ++ L A+K G + + T L+ Sbjct: 69 SYAQMSERSARMANFLRG-VGVGRGDRLLLMLPNRVELWDVMLAAMKLGAIVLPATTQLS 127 Query: 111 ESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQ 170 D + A AVV L F + + P V A G LAA + Sbjct: 128 ADDVRDRVQIGGANFAVVDSAELAKFDAL--EAPLTRLSVGAPRDGWIDLAAAYDASPQF 185 Query: 171 FEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSD--LIHTAELYARPILGIREGDVVFSAA 228 T D ++SG+T PK H H + H + +Y +G++ D+ ++ + Sbjct: 186 TPEGITLATDPMLLYFTSGTTSKPKLVEHTHQSYPVGHLSTMYW---IGLQPNDIHWNIS 242 Query: 229 KLFFAYGLGNGLIFPL-AVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLAN 287 +A + P A V R P L R PT++ ++ Sbjct: 243 SPGWAKHAWSCFFAPWNAQACVFVFNFARFVPKDTLNALVRFNITTLCAPPTVWRMLVQE 302 Query: 288 --PDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDV 345 D P ++LR AGE L +V R + +G+ I DG G TE ++ V Sbjct: 303 HLSDYP----VKLREIVGAGEPLNPEVIERVKHAWGITIRDGYGQTETTCQIGNSPGQPV 358 Query: 346 HYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWT 405 G+ G+P+PGY + LID D +T ++ L Y NN + TA + Sbjct: 359 VAGSMGRPLPGYTIELIDADDQPVTEGEISLPLAQRPLGLMTGYANNAKATAQAMRNGFY 418 Query: 406 RSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHL 465 R+ D L D+GYYVY GR+DD+ K S +SP E+ES LI HEA+ EAAVV D L Sbjct: 419 RTSDVALRRDDGYYVYVGRADDVFKSSDYRLSPFELESVLIEHEAIGEAAVVPSADALRL 478 Query: 466 IKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 PKAF+ ++ GY AG L + A + LAPYK R ++F +LPKT +GKI+R +LR Sbjct: 479 SVPKAFVTVRQGYEAGPELARAVFAFSREKLAPYKRIRRLQF-SELPKTISGKIRRVELR 537 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: 743 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: 563 Length adjustment: 35 Effective length of query: 492 Effective length of database: 528 Effective search space: 259776 Effective search space used: 259776 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