Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate RR42_RS13535 RR42_RS13535 2-aminobenzoate-CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Cup4G11:RR42_RS13535 Length = 557 Score = 304 bits (779), Expect = 5e-87 Identities = 189/518 (36%), Positives = 274/518 (52%), Gaps = 15/518 (2%) Query: 17 KIPERYNAADDLIGRNLLAGRGGKTV--YIDDAGSYT--YDELALRVNRCGSALRTTLGL 72 + PER N A +L+ R++ GRG + Y D T Y ELA NR L + L Sbjct: 31 RYPERMNCALELVERHVREGRGERVAIRYEQDGAHRTVSYAELAALSNRIAHVLTGDMKL 90 Query: 73 QPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQEL 132 P RVL+ + + +L +K G++ + LL + + ++ +A A+ + L Sbjct: 91 VPGSRVLLRGPNNLMMAACWLAVVKAGLIAVPTMPLLRAKELKQVIDRAAVSAALCDERL 150 Query: 133 LPLFAPMLGK-----VPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFWLYS 187 L P+L + +G S+ A +A + FEA T DD C ++ Sbjct: 151 REELEANLKPGGEHHCPSLTQALYFNSSGAGSVEAAMANKPDGFEACDTAADDICLIAFT 210 Query: 188 SGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVG 247 SG+TG PKGTVH H D+I +L+ R +L D+ L F +GLG L FPL VG Sbjct: 211 SGTTGQPKGTVHFHRDVIAMCDLFPRHVLKPGPDDIFCGTPPLAFTFGLGGILCFPLRVG 270 Query: 248 ATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEA 307 A+ VL AER TP ++ ++ + I + PT Y M A P L+ SAGEA Sbjct: 271 ASTVL-AERLTPESLLALIQSWRATIVFTAPTFYRQMAAL--APGYDLSSLQKSVSAGEA 327 Query: 308 LPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGA 367 LP+ + W+A G+++ DGIG TEM+HIF+S+ DV G GK VPGY +++DE Sbjct: 328 LPDATRQSWKAATGIEMTDGIGGTEMMHIFISSAGADVRPGAIGKVVPGYIAQIVDEQMQ 387 Query: 368 EITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDD 427 + G G+L + GP+ Y ++P + G W GD + + +GYY Y RSDD Sbjct: 388 PVPH-GTVGKLAVRGPTGC-RYLDDPRQANYVKDG-WNLPGDTFKADADGYYYYQARSDD 444 Query: 428 MLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTD 487 M+ +G ++ EVESAL+ HEAV E VVG D + A++VL+PG A + Sbjct: 445 MIVSAGYNIAGPEVESALMRHEAVAECGVVGMPDPERGQIVAAYVVLRPGVAASDETCAA 504 Query: 488 LKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 L+++VK +APYKYPR + FVD LP+T TGK+QRF+LR Sbjct: 505 LQSYVKAEIAPYKYPRKVIFVDALPRTETGKLQRFRLR 542 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: 778 Number of extensions: 48 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: 557 Length adjustment: 35 Effective length of query: 492 Effective length of database: 522 Effective search space: 256824 Effective search space used: 256824 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