Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate GFF2136 PS417_10895 AMP-dependent synthetase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__WCS417:GFF2136 Length = 566 Score = 196 bits (499), Expect = 1e-54 Identities = 152/490 (31%), Positives = 233/490 (47%), Gaps = 16/490 (3%) Query: 44 IDDAGS---YTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGV 100 +++ GS Y++ +LA R N+ + LR LG+ DRVL+ + + + T L A K G Sbjct: 56 VEEDGSEQRYSFQQLAARSNQVANHLRA-LGVNRGDRVLLMLGNDVALWDTMLAAFKLGA 114 Query: 101 VPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSL 160 V I LL D + R VV + + FA + + G A + Sbjct: 115 VVIPATALLNPDDLRDRIERGQVRHVVVGEAHVHKFAGLAQGCSR----ICVGSAPAGWV 170 Query: 161 AALLATG-SEQFEA-APTRPDDHCFWLYSSGSTGAPKGTVHIHSD--LIHTAELYARPIL 216 A A EQFEA T D ++SG+T PK +H H + H + +Y + Sbjct: 171 AHNAAFEYPEQFEAQGRTLATDPMLLYFTSGTTSKPKMVLHSHQSYPVGHLSTMYW---I 227 Query: 217 GIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLM-AERPTPAAVFERLRRHQPDIFY 275 G++ GD+ + + +A + L P GA + R + A+ L R+ Sbjct: 228 GLQPGDLHLNISSPGWAKHAWSCLFAPWNAGACIFIHNVARFSAPALLSALERYGVTSLC 287 Query: 276 GVPTLYASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLH 335 PT++ ++ L LR AGE L ++ + Q +G+ + DG G +E Sbjct: 288 APPTVWRMLIQEDLASYRPRLSLRELVGAGEPLNPEIIEQIQQAWGLPLRDGFGQSETTA 347 Query: 336 IFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEK 395 + + + G+ G+P+PGY++ L+D DG VA L + + Y ++PEK Sbjct: 348 LVGNTPGQLLKPGSMGRPLPGYQVALLDPDGIPGNEGEVALPLDVRPLGLMLCYEDSPEK 407 Query: 396 TAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAA 455 TA + R+GD ++ +GY + GR+DD+ K S +SP E+ESALI H AV+E A Sbjct: 408 TAEVMRDGYYRTGDTAQIDADGYITFVGRADDVFKASDYRISPFELESALIEHPAVMEVA 467 Query: 456 VVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTA 515 VV D L PKAF++L AL + A + LAPYK R IEFV +LPKT Sbjct: 468 VVPSPDPLRLAVPKAFLILAHDEPGSAALAQHILAFAREHLAPYKRVRRIEFVTELPKTI 527 Query: 516 TGKIQRFKLR 525 +GKI+R +LR Sbjct: 528 SGKIRRVELR 537 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: 760 Number of extensions: 44 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: 566 Length adjustment: 36 Effective length of query: 491 Effective length of database: 530 Effective search space: 260230 Effective search space used: 260230 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