Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate H281DRAFT_03697 H281DRAFT_03697 anthranilate--CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Burk376:H281DRAFT_03697 Length = 546 Score = 293 bits (750), Expect = 1e-83 Identities = 177/522 (33%), Positives = 267/522 (51%), Gaps = 15/522 (2%) Query: 14 PAIKIPERYNAADDLIGRNLLAGRGGK----TVYIDDAGSYTYDELALRVNRCGSALRTT 69 P + P R+N A +L+ R + AG G + ++ ++ + +Y EL VNR L Sbjct: 29 PDVAYPARFNCATELLARTIEAGHGERAAIWSLVDNEPRATSYKELLAMVNRSAHVLVDE 88 Query: 70 LGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVS 129 +GLQP +R+L+ + + L A+K G+V + LL + + ++ + A+ Sbjct: 89 MGLQPGNRILLRGPNTLQMAVAALAALKVGLVAVPTMPLLRAKELKQIIAKAQVSAALCD 148 Query: 130 QELLPLFAPMLGK-----VPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFW 184 L A L+ ++ DSL L F A T DD C Sbjct: 149 ARLTEELARCNDPQDEFYCAELKQTLLFHDDAVDSLDTLAINKPADFAACDTAADDVCLI 208 Query: 185 LYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPL 244 ++SG+TGAPKG +H H D++ +L+ R +L D+ L F +GLG L FPL Sbjct: 209 AFTSGTTGAPKGCMHFHRDVLAMCDLFPRHVLKPSASDIFCGTPPLAFTFGLGGLLCFPL 268 Query: 245 AVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSA 304 VGA+ VL+ E+ TP + + + R I + PT Y M P + L+ SA Sbjct: 269 RVGASTVLI-EKLTPETLLQTVERFHATIMFTAPTFYRQMA--PLVARHDVSSLQKTVSA 325 Query: 305 GEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDE 364 GEALP+ R W+ G+D++DGIG TE++HIF+S + ++ G+ VPGY ++ +D Sbjct: 326 GEALPDSTRRLWRDATGIDMIDGIGGTELIHIFVSAQGDEIRPHAIGRAVPGYIVQAVD- 384 Query: 365 DGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGR 424 D + G G+L + GP+ + E+ W GD ++ +GY Y R Sbjct: 385 DAMQPVAPGTIGKLAVRGPTGC--RYLADERQMKFVRDGWNLPGDSVYLDADGYVFYQAR 442 Query: 425 SDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEAL 484 +DDM+ +G +S EVES L+ HEAV E V+G DE KAF+VL PGY + L Sbjct: 443 ADDMIVSAGYNISGPEVESVLLQHEAVAECGVIGVPDETRGQIVKAFVVLNPGYTCDDNL 502 Query: 485 RTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 L+ VKN +APYKYPR + FVD LP+T TGK++RF+LR+ Sbjct: 503 VAQLQDFVKNTVAPYKYPRVVAFVDSLPRTETGKLKRFELRT 544 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: 689 Number of extensions: 37 Number of successful extensions: 6 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: 546 Length adjustment: 35 Effective length of query: 492 Effective length of database: 511 Effective search space: 251412 Effective search space used: 251412 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