Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate Dsui_3212 Dsui_3212 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__PS:Dsui_3212 Length = 555 Score = 191 bits (486), Expect = 5e-53 Identities = 151/524 (28%), Positives = 234/524 (44%), Gaps = 44/524 (8%) Query: 40 KTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGG 99 + YI+ TY EL + L+ L L RV + + + + +P GA++ G Sbjct: 39 RVAYINMGVGITYGELDRLSRDFAAYLQDVLKLPQGARVALMMPNLLQYPVCMFGALRAG 98 Query: 100 VVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDS 159 V + N L T + E+ L DS A V+ + L VP L+H++V D Sbjct: 99 YVVVNCNPLYTHRELEHQLKDSGAEAIVIVENFAHTLEQALPLVPGLKHVIVTSLG--DM 156 Query: 160 LAALLATGSE-------------------QFEAAPTRP------------DDHCFWLYSS 188 L AL T +F+AA R +D + Y+ Sbjct: 157 LGALKGTVVNLVVRHVKKMVPAWKLPRHVKFKAAMARGKGATLRPVQVGHEDIAYLQYTG 216 Query: 189 GSTGAPKGTVHIHSDLI---HTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLA 245 G+TG KG + +H ++I A + P L ++ ++ +A L+ + L + L Sbjct: 217 GTTGVAKGAMLLHRNIIANLQQAHAWIEPFLH-KDQQLIITALPLYHIFSLTANCLTFLK 275 Query: 246 VGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAG 305 +GAT VL+ + L +++ + GV TL+ ++L NPD K LRA G Sbjct: 276 IGATNVLITNPRDIPGFVKELAQYKFTVITGVNTLFNALLNNPDFAKLDFSALRAALGGG 335 Query: 306 EALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHY-GTSGKPVPGYRLRLIDE 364 A+ + V ++W+ G +++ G TE N + G G P+ + + D+ Sbjct: 336 MAVQKSVAQKWRQVTGKPLIEAYGLTETSPAATINPLDLGEFNGAIGLPISSTEIVIRDD 395 Query: 365 DGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGE-WTRSGDKYLVNDEGYYVYAG 423 G ++ G AGE+ I GP YW P++TA F + + R+GD +++++G+ Sbjct: 396 LGNDLPV-GQAGEICIRGPQVMKGYWLRPDETATVFYADGFLRTGDVGVMDEKGFVRIVD 454 Query: 424 RSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEA 483 R DM+ VSG V P EVE+ + H AV+E A VG E K F+VLK Sbjct: 455 RKKDMILVSGFNVYPNEVEAVVAMHPAVMEVAAVGVPSEHSGEAVKIFVVLKD----KSV 510 Query: 484 LRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRSA 527 + L AH K L YK P +EF DDLPKT GKI R L+ A Sbjct: 511 TKEQLIAHCKENLTGYKVPHLVEFRDDLPKTNVGKILRRALKEA 554 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: 656 Number of extensions: 35 Number of successful extensions: 7 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: 555 Length adjustment: 35 Effective length of query: 492 Effective length of database: 520 Effective search space: 255840 Effective search space used: 255840 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