Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate BPHYT_RS35445 BPHYT_RS35445 2-aminobenzoate-CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__BFirm:BPHYT_RS35445 Length = 546 Score = 293 bits (749), Expect = 1e-83 Identities = 181/526 (34%), Positives = 268/526 (50%), Gaps = 23/526 (4%) Query: 14 PAIKIPERYNAADDLIGRNLLAG-RGGKTVYIDDAGS---YTYDELALRVNRCGSALRTT 69 P + P R N A +L+ R + AG R ++ D G+ TY EL VNR L Sbjct: 29 PDVAYPARLNCASELLDRTIDAGHRDDPAIWSDVDGAPRATTYGELLALVNRSAHVLVDE 88 Query: 70 LGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVS 129 +GLQP +RVL+ + + T L A+K G+V + LL + + ++ + A+ Sbjct: 89 MGLQPGNRVLLRGPNTLHMAVTALAALKVGLVVVPTMPLLRAKELKQIIDKAQVGAALCD 148 Query: 130 QELLPLFAPMLGKVPTLEHLVVAGGAGE---------DSLAALLATGSEQFEAAPTRPDD 180 L L + E G + DSL L + F A T DD Sbjct: 149 ARL----TAELARCSDPEDEFYCAGLMQTRLFHDDSPDSLDTLAVNKPDHFTACDTAADD 204 Query: 181 HCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGL 240 C ++SG+TGAPKG +H H D++ +L+ R +L D+ L F +GLG L Sbjct: 205 VCLIAFTSGTTGAPKGCMHFHRDVVAMCDLFPRHVLKPTSSDIFCGTPPLAFTFGLGGLL 264 Query: 241 IFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRA 300 FPL VGA+ VL+ E+ TP + + + R + + PT Y M P L+ Sbjct: 265 CFPLRVGASTVLI-EKLTPETLLQTVERFHATVMFTAPTFYRQMA--PLVAHHDVSSLKK 321 Query: 301 CTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLR 360 SAGEALP+ R W+ G+D++DGIG TE++HIF+S + ++ G+ VPGY ++ Sbjct: 322 TVSAGEALPDSTRRLWRDATGIDMIDGIGGTELIHIFISAQGDEIRPNAIGRAVPGYAVQ 381 Query: 361 LIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYV 420 +D+D + G G+L + GP+ + E+ W GD ++++GY Sbjct: 382 AVDDDMQPVAP-GTIGKLAVRGPTGC--RYLADERQMKFVRDGWNLPGDSVYLDEDGYVF 438 Query: 421 YAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGA 480 Y R+DDM+ +G +S EVES L+ H+AV E V+G DE KAF+V+ PGY Sbjct: 439 YQARADDMIVSAGYNISGPEVESVLLQHDAVSECGVIGVPDETRGQIVKAFVVVNPGYER 498 Query: 481 GEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 + L L+ VKN +APYKYPR I FVD LP+T TGK++RF+LR+ Sbjct: 499 DDKLVAQLQEFVKNSVAPYKYPRDIVFVDSLPRTETGKLKRFELRT 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: 735 Number of extensions: 41 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: 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