Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate PP_2213 PP_2213 putative acyl-CoA synthetase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Putida:PP_2213 Length = 561 Score = 186 bits (471), Expect = 3e-51 Identities = 166/525 (31%), Positives = 250/525 (47%), Gaps = 36/525 (6%) Query: 20 ERYNAADDLIGRNLLAGRGGKTVYIDD----AGSYTYDELALRVNRCGSALRTTLGLQPK 75 E NA + R+ AG G + +D + Y++D+L ++ R + L+ G+ Sbjct: 39 EALNACVECCDRH--AGDGKLALIHEDRDGNSACYSFDQLQVQAARFANVLKAQ-GVGAG 95 Query: 76 DRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPL 135 DRV + + T L + G V + T E+ L S ARV V Sbjct: 96 DRVAGLMPRTPELLVTILATWRLGAVYQPLFTAFGPKAIEHRLEQSHARVVVTDSHNRAK 155 Query: 136 FAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPK 195 + PT+ + V +GE L ++ E +D +++SG+TG P Sbjct: 156 LDDVHA-CPTI--ITVKARSGELDFQQCLERAADVCEPVMRSGNDPFLLMFTSGTTG-PA 211 Query: 196 GTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAE 255 + + I + Y R + + D ++ A +AYGL + PL++G A + Sbjct: 212 KPLEVPLRAIVAFQGYMRDAIELLPEDNFWNLADPGWAYGLYYAVTGPLSLGH-ATTFYD 270 Query: 256 RP----TPAAVFERLRRHQPDIFYGVPTLYASMLA---NPDCPKEGELRLRACTSAGEAL 308 P + A V ++L G PT Y ++A + P +G RLR +SAGE L Sbjct: 271 GPFSVESCARVIDKLGITN---LAGSPTAYRLLIAAGKDFSAPIKG--RLRVVSSAGEPL 325 Query: 309 PEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAG---DVHYGTSGKPVPGYRLRLIDED 365 +V R + GV I D G TE L + L N G VH G++G +PG+R+ ++DE Sbjct: 326 NPEVIRWFADELGVTIHDHYGQTE-LGMVLCNHHGLQHPVHLGSAGYAIPGHRIVVVDEQ 384 Query: 366 GAEITTAGVAGELQISGPSSAVMYWNN----PEKTAATFMGEWTRSGDKYLVNDEGYYVY 421 G E+ AG G L + S + ++ P K F+G++ SGD +N +G + Sbjct: 385 GNELP-AGQPGILAVDREQSPLCWFGGYHGLPTKA---FVGKYYLSGDTVELNPDGSISF 440 Query: 422 AGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAG 481 GRSDD++ SG V P +VESALI H AV+EAAV+G D + KAF+VL GY Sbjct: 441 VGRSDDVITTSGYRVGPFDVESALIEHPAVIEAAVIGKPDPERTELIKAFVVLASGYAGS 500 Query: 482 EALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526 L L+ HV+ L + YPR IEFV +LPKT +GK+QRF LR+ Sbjct: 501 VELEETLRQHVRQRLYAHAYPREIEFVSELPKTPSGKLQRFILRN 545 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: 777 Number of extensions: 37 Number of successful extensions: 4 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: 561 Length adjustment: 35 Effective length of query: 492 Effective length of database: 526 Effective search space: 258792 Effective search space used: 258792 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