Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate GFF3986 HP15_3926 acyl-CoA synthetase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Marino:GFF3986 Length = 554 Score = 173 bits (438), Expect = 2e-47 Identities = 140/480 (29%), Positives = 215/480 (44%), Gaps = 38/480 (7%) Query: 71 GLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ 130 G++ DRVL+ + + + ++ ++ V I +N + ++ E+ + D+ A V + Q Sbjct: 68 GVKKGDRVLLYMQNSPQYVISYYAILRADAVVIPVNPMNRSAELEHFIADTGATVCLAGQ 127 Query: 131 ELLPLFAPMLGKVPTLEHLVVAGGAG------EDSLAALLAT--------GSEQFEAA-- 174 EL APM+G L+ +VVA + + L A +A G +E A Sbjct: 128 ELAGFIAPMIGD-SNLDQVVVASYSTYIDPETDLDLPAEVAAPVWSRDLPGVVTWEVAMA 186 Query: 175 --------PTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFS 226 PDD YSSG+TGAPKG +H H ++ TA R + D V Sbjct: 187 AGYAPGPHTATPDDLAVIPYSSGTTGAPKGCMHTHRSVMATA--IHRIFWNLTTPDSVQL 244 Query: 227 AAKLFF-AYGLGNGLIFPLAVGATAVLMA--ERPTPAAVFERLRRHQPDIFYGVPTLYAS 283 A FF G+ + P+A GA +V+M +R T + + ER ++ + + T+ Sbjct: 245 ATLPFFHVTGMTGSMNGPIAAGAASVIMTRWDRTTASRLIER---YKVTGWTNIVTMAVD 301 Query: 284 MLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAG 343 L+NPD + L G +P V + + G+D ++G G +E + N Sbjct: 302 FLSNPDIGQYDLSSLNMIGGGGATMPSAVAEKLKRMTGLDYIEGYGLSETMAATHINPNA 361 Query: 344 DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMG- 402 G PV R+ID D E G GE+ GP YWN P +T A F+ Sbjct: 362 HPKSQCLGIPVFDVDSRIIDVDTLEEKGPGETGEIVSCGPQVTRGYWNRPSETEAAFVEI 421 Query: 403 ---EWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGW 459 ++ R+GD +++GY+ R M+ SG V P EVE + H A+ E ++ Sbjct: 422 DGKQFFRTGDLGYYDEDGYFFMVDRVKRMINASGYKVWPSEVEGMMYRHPAIHEVCIISA 481 Query: 460 EDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKI 519 D KA IVL P G+ D+ A K +A YK P I+FVD LPK+ TGK+ Sbjct: 482 PDPKRGETVKACIVLTP-EAEGQTSAGDIIAWCKEQMATYKVPTMIDFVDQLPKSPTGKL 540 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: 736 Number of extensions: 34 Number of successful extensions: 7 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: 554 Length adjustment: 35 Effective length of query: 492 Effective length of database: 519 Effective search space: 255348 Effective search space used: 255348 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