Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate AO353_19945 AO353_19945 acetyl-CoA synthetase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19945 Length = 588 Score = 187 bits (476), Expect = 7e-52 Identities = 151/493 (30%), Positives = 233/493 (47%), Gaps = 19/493 (3%) Query: 51 TYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLT 110 +Y L+L NR + L+T LG+ P +R+ V G++ LG +K G V + Sbjct: 81 SYARLSLLSNRFANVLKT-LGVVPGERLFVLCGRGLELYLGVLGGLKLGCVVSPLFCAFG 139 Query: 111 ESDYEYMLTDSAARVAVVSQELLP-LFAPMLGKVPTLEHLVV---AGG-----AGEDSLA 161 E L V + S+ L A + ++P L+H+++ GG G SL Sbjct: 140 PEPIETRLRLGEGSVLLTSETLYRHKVAAIRERLPALKHVLLYDEEGGNTTPVEGTLSLH 199 Query: 162 ALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREG 221 LLA ++ FE A T D ++SG+TG PKG +H+H ++ T + + L + Sbjct: 200 RLLANATDHFEIAHTTADSPALLHFTSGTTGTPKGVLHVHGAVL-THRVTGKYALDLHPD 258 Query: 222 DVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPT-L 280 D+ + +A + G G+I PL +G T+V+ + L + Q ++Y PT + Sbjct: 259 DIYWCSADPGWVTGTSYGIIAPLLLGVTSVVEGREFDAERWYRTLEKQQVTVWYTAPTAI 318 Query: 281 YASMLANPDCPKEGELR-LRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLS 339 M A + LR S GE L + Q G+ I D TE I ++ Sbjct: 319 RLLMKAGAELAHSHRFPCLRFIASVGEPLNPEAVWWGQEVLGLPIHDNWWQTETGGIMIA 378 Query: 340 NR-AGDVHYGTSGKPVPGYRLRLIDEDGA-EITTAG--VAGELQISGPSSAVM--YWNNP 393 N A + G+ GKP+PG ++ A E+ G GEL + P A+ Y Sbjct: 379 NTVAMTIKPGSMGKPLPGVEAAVVVRGAAGELDYLGDNEVGELALKQPWPAMFRTYLGQE 438 Query: 394 EKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLE 453 E+ F+ W SGD + +GYY + GRSDD++K +G + P EVES+L+ H AV E Sbjct: 439 ERYRQCFVAGWYLSGDLVRRDADGYYWFIGRSDDVIKSAGHLIGPFEVESSLMEHPAVAE 498 Query: 454 AAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPK 513 AAV+G D K F+ LK G+ A +AL +L H + L P+ +EFV+ LP Sbjct: 499 AAVIGKPDPLLGETVKVFVSLKSGFTASQALHDELLGHGRKRLGAVVAPKELEFVEALPH 558 Query: 514 TATGKIQRFKLRS 526 T +GK+ R L++ Sbjct: 559 TRSGKLMRRLLKA 571 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: 835 Number of extensions: 58 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: 588 Length adjustment: 36 Effective length of query: 491 Effective length of database: 552 Effective search space: 271032 Effective search space used: 271032 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: 53 (25.0 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