Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate H281DRAFT_00369 H281DRAFT_00369 benzoate-CoA ligase (EC 6.2.1.25)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Burk376:H281DRAFT_00369 Length = 534 Score = 565 bits (1456), Expect = e-165 Identities = 309/520 (59%), Positives = 364/520 (70%), Gaps = 21/520 (4%) Query: 19 PERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRV 78 P R+N A L N A R KT YIDD+G TY EL R R SALR LG+ P++RV Sbjct: 20 PARFNFAAHLFALN--APRAAKTAYIDDSGHMTYGELEDRARRFSSALRG-LGVHPEERV 76 Query: 79 LVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAP 138 L+ +LD + P FLGA+ GVVP+ NTLLT +DY YMLT S AR + S L+P Sbjct: 77 LLVMLDTVSLPIAFLGALYAGVVPVVANTLLTSADYVYMLTHSHARAVIASSVLIPNVTQ 136 Query: 139 MLGKVPTLEH----LVVAGGAGE----DSLAA-----LLATGSEQFEAAPTRPDDHCFWL 185 + T EH L+V+ A + LAA L+ + +AA T DD FWL Sbjct: 137 AM---ETAEHDGCQLIVSNRAAPAPEGEPLAAPVLEDLIDAATPALKAATTGCDDIAFWL 193 Query: 186 YSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLA 245 YSSGSTG PKGTVH H++L TAELYA+P+LGI E DVVFSAAKLFFAYGLGN L FPL+ Sbjct: 194 YSSGSTGKPKGTVHTHANLYWTAELYAKPVLGIVESDVVFSAAKLFFAYGLGNALTFPLS 253 Query: 246 VGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAG 305 VGATAVLMAERPT AVF RL RH+P +FYGVPTLYASML +P+ P ++ +R CTSAG Sbjct: 254 VGATAVLMAERPTADAVFSRLTRHRPTVFYGVPTLYASMLVSPNLPARDDVAMRVCTSAG 313 Query: 306 EALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDED 365 EALP ++G R+ FG +ILDGIGSTEMLHIFLSNRAG+V YGT+G+PVPGY + L D+ Sbjct: 314 EALPREIGERFTRHFGCEILDGIGSTEMLHIFLSNRAGEVEYGTTGRPVPGYEVELRDDS 373 Query: 366 GAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRS 425 G + G G+L I GPS+A+MYW N EKT ATF+GEW RSGDKY G YVYAGRS Sbjct: 374 GRAVGD-GEVGDLFIKGPSAALMYWCNREKTRATFLGEWIRSGDKYSRLPNGCYVYAGRS 432 Query: 426 DDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALR 485 DDMLKVSG YVSP+EVE L+ H+AVLEAAVVG D L+K +AF+VLK + E L Sbjct: 433 DDMLKVSGQYVSPVEVEMVLVQHDAVLEAAVVG-IDHGGLVKTRAFVVLKREFSPSEILV 491 Query: 486 TDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 +LKA VK LAP+KYPR I FVDDLPKTATGKIQRFKLR Sbjct: 492 DELKAFVKGRLAPHKYPRDIVFVDDLPKTATGKIQRFKLR 531 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: 882 Number of extensions: 35 Number of successful extensions: 5 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: 534 Length adjustment: 35 Effective length of query: 492 Effective length of database: 499 Effective search space: 245508 Effective search space used: 245508 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