Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate BPHYT_RS13365 BPHYT_RS13365 4-hydroxybenzoate--CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__BFirm:BPHYT_RS13365 Length = 530 Score = 565 bits (1455), Expect = e-165 Identities = 313/525 (59%), Positives = 366/525 (69%), Gaps = 22/525 (4%) Query: 10 SNTPPAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTT 69 + PPA+ +N A L N R KT YIDD GS TY EL R R SALRT Sbjct: 16 AEAPPAL-----FNFAAYLFRLN--ETRATKTAYIDDTGSITYGELEERARRFASALRT- 67 Query: 70 LGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVS 129 LG+ P++RVL+ +LD I P FLGA+ GVVP+ NTLLT +DY YMLT S AR + S Sbjct: 68 LGVHPEERVLLVMLDTIALPVAFLGALYAGVVPVVANTLLTPADYVYMLTHSHARAVIAS 127 Query: 130 QELLPLFAPMLGKVPTLEH-----LVVAGGAGEDSLAALLA----TGSEQFEAAPTRPDD 180 L+ L + EH +V GE LA LL + +AA T DD Sbjct: 128 GALVQNVTQALD---SSEHDGCQLIVSQPCEGEPLLAPLLEELIDAAAPAAKAAATGCDD 184 Query: 181 HCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGL 240 FWLYSSGSTG PKGTVH H++L TAELYA+PILGI E DVVFSAAKLFFAYGLGNGL Sbjct: 185 IAFWLYSSGSTGKPKGTVHTHANLYWTAELYAKPILGIAESDVVFSAAKLFFAYGLGNGL 244 Query: 241 IFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRA 300 FPL+VGATA+LMAERPT A+F RL +H+P +FYGVPTLYA+ML +P+ P ++ +R Sbjct: 245 TFPLSVGATAILMAERPTADAIFMRLVKHRPTVFYGVPTLYANMLVSPNLPARADVAMRI 304 Query: 301 CTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLR 360 CTSAGEALP ++G R+ A FG +ILDGIGSTEMLHIFLSNRAG V YGT+G+PVPGY + Sbjct: 305 CTSAGEALPREIGERFTAHFGCEILDGIGSTEMLHIFLSNRAGAVEYGTTGRPVPGYEVE 364 Query: 361 LIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYV 420 L D+ G + G G+L I GPS+AVMYWNN EKT ATF+GEW RSGDKY G YV Sbjct: 365 LRDDAGHAVAD-GEVGDLYIKGPSAAVMYWNNREKTRATFLGEWIRSGDKYCRLANGCYV 423 Query: 421 YAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGA 480 YAGRSDDMLKVSG YVSP+EVE L+ H AVLEAAVVG D L+K +AF+VLK + A Sbjct: 424 YAGRSDDMLKVSGQYVSPVEVEMVLVQHGAVLEAAVVG-VDHGGLVKTRAFVVLKREFAA 482 Query: 481 GEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 E L +LKA VK+ LAP+KYPR I FVDDLPKTATGKIQRFKLR Sbjct: 483 SEILAEELKAFVKDRLAPHKYPRDIVFVDDLPKTATGKIQRFKLR 527 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: 827 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: 530 Length adjustment: 35 Effective length of query: 492 Effective length of database: 495 Effective search space: 243540 Effective search space used: 243540 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