Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_011384660.1 AMB_RS11445 2-aminobenzoate-CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >NCBI__GCF_000009985.1:WP_011384660.1 Length = 551 Score = 247 bits (631), Expect = 7e-70 Identities = 176/525 (33%), Positives = 254/525 (48%), Gaps = 12/525 (2%) Query: 6 VADHSNTPPAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSA 65 V D+S P P+R NAA LI + AG G K V+ G+++Y L R R Sbjct: 32 VFDYS-APHLSHYPDRINAAAALIDTAVAAGFGAKPVFHYGEGTWSYAHLLDRAERIARV 90 Query: 66 LRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARV 125 L L P RVL+ + +L +K G + + LL + Y++ + + Sbjct: 91 LTEDFWLVPGARVLLRSANTPMLVACWLAVLKAGGICVTTMPLLRAKELSYIVEKARVSI 150 Query: 126 AVVSQELLPLFAPMLGKVPTLEHL-----VVAGGAGEDSLAALLATGSEQFEAAPTRPDD 180 A+ +L K+ L H+ + G E L F T DD Sbjct: 151 ALCELDLAEEMDLTRQKMAELRHVAYFTPLCDGAKAEADLDRRAEAKPTGFANVDTAADD 210 Query: 181 HCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGL 240 ++SG+TG PKG +H H D++ + + + R + +VV + + F YG + Sbjct: 211 VALITFTSGTTGNPKGAMHFHRDILASCDCWPRRHT-LEPDEVVIGSPSIAFTYGKAAFM 269 Query: 241 IFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRA 300 ++PL ATAVL+ +PTP + E ++RH+ Y VPT + +ML K LR Sbjct: 270 MYPLRHRATAVLVP-KPTPELILEGIQRHRATSLYAVPTAFNAMLGMVG--KYDISSLRK 326 Query: 301 CTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLR 360 +SAGE L + W R GV +++GIG TEML F+ A G +G PV GY Sbjct: 327 ASSAGEHLRPKLYDDWLERTGVKLVNGIGMTEMLTHFICQSADVAKPGATGFPVDGYTAC 386 Query: 361 LIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYV 420 ++D+D + G G L + GP+ Y ++ + AA W +GD + EG++ Sbjct: 387 ILDDDFNPLPV-GSKGRLAVRGPTGC-RYLDDQARQAAFVRNGWNVTGDIMEQDAEGWFW 444 Query: 421 YAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGA 480 Y RSDDM+ SG +S EVE A++ H V E AV+G DE +A IVL A Sbjct: 445 YVDRSDDMIVSSGYNISAQEVERAVLEHPKVAECAVIGVPDEARGTIVRACIVLDNPSQA 504 Query: 481 GEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 E L +++ VK +APYKYPR I FVD LPKT TGKIQRF+LR Sbjct: 505 SELLAEEIQNFVKANIAPYKYPREIRFVDFLPKTQTGKIQRFRLR 549 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: 764 Number of extensions: 46 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: 551 Length adjustment: 35 Effective length of query: 492 Effective length of database: 516 Effective search space: 253872 Effective search space used: 253872 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