Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate 8499484 DvMF_0256 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Miya:8499484 Length = 583 Score = 181 bits (459), Expect = 7e-50 Identities = 135/487 (27%), Positives = 215/487 (44%), Gaps = 35/487 (7%) Query: 71 GLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ 130 G++ D+V + + + F +K G V + N L E + + + DS AR + Sbjct: 75 GVRRGDKVSIMLPNLPQTVIAFWAVLKAGGVVVMTNPLYMEKELVHQIHDSGARFMIALD 134 Query: 131 ELLPLFAPMLGKVPTLEHLVVAGGAG---------------EDSLAAL------------ 163 + P P+ K+ ++ + G G E + L Sbjct: 135 LVWPKIEPLREKLGIDKYFLTRIGDGLAFPLNFLYAFKAKREGTWRELPFDGRHVLPWKT 194 Query: 164 LATGSEQFEAAPTRP-DDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGD 222 L G + P +D Y+ G+TG KG + H ++ + + R+ D Sbjct: 195 LLKGKVRHSTTTCNPTEDLAVLQYTGGTTGISKGVMLTHHNMSVNVQQITTILGDARDMD 254 Query: 223 VVFSAAKLFF-AYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLY 281 F +F YGL L P A+ AT V R P V +++H+P IF G P++Y Sbjct: 255 HCFLGLMPYFHVYGLTTCLTLPTALAATIVPFP-RYVPRDVLVGIQKHKPTIFPGAPSIY 313 Query: 282 ASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHI-FLSN 340 S++ + +R C S +P + +R++ G +++G G TE + L+ Sbjct: 314 ISLMQQKEVGDYDLTSIRYCISGSAPMPVEHIKRFRELTGAQVIEGFGLTEASPVTHLNP 373 Query: 341 RAGDVHYGTSGKPVPGYRLRLIDEDGAEITT-AGVAGELQISGPSSAVMYWNNPEKTAAT 399 G G+ G P P R++D + ++ AG GEL I GP YWN P++TA T Sbjct: 374 IHGVSKTGSIGIPFPDTEARIVDMEVGQVPLPAGKVGELIIRGPQVMKGYWNRPDETANT 433 Query: 400 FMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGW 459 W +GD +++++GY+ R DM V G V P E++ L H + EA VG Sbjct: 434 LRNGWLYTGDIAIMDEDGYFTIVDRKKDMFLVGGYNVYPREIDEVLHEHPKIKEAVTVGV 493 Query: 460 EDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKI 519 KAF+V+KPG + + ++ AH + LA YK P+ +EF DDLPKT GK+ Sbjct: 494 PHPTRGEMIKAFVVVKPG---EKLTKAEVVAHCREKLASYKVPKQVEFRDDLPKTVVGKV 550 Query: 520 QRFKLRS 526 R LR+ Sbjct: 551 LRRILRT 557 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: 746 Number of extensions: 44 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 527 Length of database: 583 Length adjustment: 36 Effective length of query: 491 Effective length of database: 547 Effective search space: 268577 Effective search space used: 268577 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