Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate HSERO_RS00095 HSERO_RS00095 AMP-dependent synthetase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__HerbieS:HSERO_RS00095 Length = 539 Score = 204 bits (518), Expect = 9e-57 Identities = 166/530 (31%), Positives = 252/530 (47%), Gaps = 22/530 (4%) Query: 12 TPPAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAG----SYTYDELALRVNRCGSALR 67 +P +IP +N A R G G + +DA SY+YD+L + +R +ALR Sbjct: 12 SPYEWQIPTHFNIAQAACDR-WADGSGRTAIICEDADGSVTSYSYDQLKILSDRFANALR 70 Query: 68 TTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAV 127 G+ DR+ + + I+ T L A K G + + + L Y L +S A VA+ Sbjct: 71 AA-GVGRGDRIGIYLSQRIETVITHLAAYKLGAITVPLFYLFGPDAIAYRLDNSGA-VAL 128 Query: 128 VSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQFEAAP-------TRPDD 180 V+ A + G++P L +V D + ++ AAP T DD Sbjct: 129 VTDASGMEKATLAGELPALR--LVFCVESSDLVLPQTTDFWDRLHAAPAELDPVLTLADD 186 Query: 181 HCFWLYSSGSTGAPKGTVHIHSDLI-HTAELYARPILGIREGDVVFSAAKLFFAYGLGNG 239 +Y+SG+TG KG +H H L+ H + +EGD ++ A + GL + Sbjct: 187 PAMIIYTSGTTGKAKGALHAHRVLLGHLPGVEVSHDSFPQEGDRFWTPADWAWIGGLLDV 246 Query: 240 LIFPLAVGATAVLMA-ERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRL 298 L+ L G V E+ A VF L RHQ + PT + + + L Sbjct: 247 LLPSLYHGVAVVARRLEKFDAAEVFGLLARHQIRNVFFPPTALKMLRGAATVRAQADFSL 306 Query: 299 RACTSAGEALPEDVGRRWQARFGVDILDGIGSTEM-LHIFLSNRAGDVHYGTSGKPVPGY 357 R+ S GE L +D+ + GV I + G TE L + S+ G+ G+ VPG+ Sbjct: 307 RSVASGGETLGDDLIAWGREALGVTINEFYGQTECNLVVSSSSHCYPSVSGSMGRAVPGH 366 Query: 358 RLRLIDEDGAEITTAGVAGELQISGPSSAVM--YWNNPEKTAATFMGEWTRSGDKYLVND 415 ++++DE G ++ G G + I P + YW N E T F G++ +GD +++ Sbjct: 367 VVQIVDEQG-QVLPHGTVGNIAIRAPDPVMFLRYWRNEEATREKFAGDFLLTGDLGSMDE 425 Query: 416 EGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLK 475 +GY Y GR+DD++ +G + P +E L+ H AV AAVVG +D KAF+VLK Sbjct: 426 QGYIRYLGRNDDVITSAGYRIGPAAIEECLMRHPAVRIAAVVGVKDALRTEVVKAFVVLK 485 Query: 476 PGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 G EAL+ +L+ HV+ LA ++YPR I FV LP TATGKI R L+ Sbjct: 486 DGVTPDEALKAELQQHVRAQLAAHEYPRLISFVAALPTTATGKIMRKTLK 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: 732 Number of extensions: 27 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: 539 Length adjustment: 35 Effective length of query: 492 Effective length of database: 504 Effective search space: 247968 Effective search space used: 247968 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