Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate RR42_RS07520 RR42_RS07520 4-hydroxybenzoate--CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Cup4G11:RR42_RS07520 Length = 566 Score = 622 bits (1604), Expect = 0.0 Identities = 321/513 (62%), Positives = 378/513 (73%), Gaps = 7/513 (1%) Query: 18 IPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDR 77 +P RYNAA DL+ RNL AGR K Y+DDAG ++ L R R +AL G++P++R Sbjct: 30 LPARYNAAADLLSRNLAAGRADKVAYVDDAGQLSFAALDQRCRRFAAALLHA-GIRPEER 88 Query: 78 VLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFA 137 +L+C LD IDFPT FLG + GVVP+A+NTLLT DY YML SAAR AVVS L + Sbjct: 89 LLLCALDTIDFPTVFLGCLLAGVVPVAVNTLLTVDDYAYMLDHSAARAAVVSAPLASVMR 148 Query: 138 PMLGKVPTLEHLVVA----GGAGED-SLAALLATGSEQFEAAPTRPDDHCFWLYSSGSTG 192 +GK T L++A G AG S+A + G+ AA TRPDD FWLYSSGSTG Sbjct: 149 EAIGKAGTAPALILAAPDAGSAGPGPSVAEMAGQGTALEGAAATRPDDIAFWLYSSGSTG 208 Query: 193 APKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVL 252 PKGTVH H +L HTA+LYAR +LG+RE DVVFSAAKLFFAYGLGN L FPLAVGAT VL Sbjct: 209 RPKGTVHTHGNLFHTADLYARQVLGLREDDVVFSAAKLFFAYGLGNALTFPLAVGATTVL 268 Query: 253 MAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPEDV 312 MAERPTP AVF RLR +P +F GVPTLYA MLA D P ++ LR CTSAGEALP+D+ Sbjct: 269 MAERPTPQAVFRRLREQRPTVFCGVPTLYAGMLAASDLPGRPDVALRVCTSAGEALPKDI 328 Query: 313 GRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTA 372 G R++A FG DILDGIGSTEMLHIFLSNR GDV YGT+GKPVPGY LRL+DE G + Sbjct: 329 GERFRAHFGCDILDGIGSTEMLHIFLSNRPGDVRYGTTGKPVPGYALRLLDEAG-QPCAP 387 Query: 373 GVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVS 432 G G+L I GPS+A+MYW N +KT TF+GEWTRSGDKY + +GY++YAGRSDDMLKV Sbjct: 388 GEIGDLFIKGPSAALMYWGNRDKTRDTFVGEWTRSGDKYQQDADGYFIYAGRSDDMLKVG 447 Query: 433 GIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHV 492 GIYVSP EVE+ L H AVLEAAV+G D D L+KPKAF+VL+PG E + +L+A V Sbjct: 448 GIYVSPFEVEAVLALHPAVLEAAVIGVADADELVKPKAFVVLRPGRSWHEGMAAELQAFV 507 Query: 493 KNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 K+ LAPYKYPR IE V +LPKTATGKIQRF+LR Sbjct: 508 KSRLAPYKYPRQIECVAELPKTATGKIQRFRLR 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: 947 Number of extensions: 34 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