Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate RR42_RS06210 RR42_RS06210 AMP-binding protein
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Cup4G11:RR42_RS06210 Length = 577 Score = 206 bits (524), Expect = 2e-57 Identities = 162/506 (32%), Positives = 238/506 (47%), Gaps = 31/506 (6%) Query: 49 SYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTL 108 SY+Y + +R ALRT LG+ DRV + + I+ + + G + + ++ L Sbjct: 62 SYSYAFIQAEADRLCRALRT-LGVARGDRVGIVMPQRIETVIAHMAIYQLGAIAMPLSML 120 Query: 109 LTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAG---GAGEDSLAALLA 165 Y L S A VA+ + + + P L ++ AG G E ALLA Sbjct: 121 FGPEALAYRLQHSEACVAIADESSIDNVLAARAECPALATVIGAGAAVGRAEHDWDALLA 180 Query: 166 TGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVF 225 F A T+ D+ +Y+SG+TG PKG + H LI + D VF Sbjct: 181 AELPAFTAVVTKADEAAVLIYTSGTTGPPKGALIPHRALIGNLPGFVCSQNWFPHADDVF 240 Query: 226 -SAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASM 284 S A + GL + L+ L G T V R + FE + R++ + PT M Sbjct: 241 WSPADWAWTGGLWDALMPTLYFGKTIVGYQGRFSAQTAFELMARYRVTNTFLFPTALKQM 300 Query: 285 LANPDCPKEG-ELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIF----LS 339 + P+ +L LRA SAGEA+ E V + GV + + G TE+ +I Sbjct: 301 MKTCPAPRAHYQLHLRALMSAGEAVGETVFAWCRDALGVVVNEMFGQTEINYIVGNCTAQ 360 Query: 340 NRAGDVHY----GTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISG--------PSSAV 387 N G + G+ G+P PG+R+ ++D++G AG GE+ + P + Sbjct: 361 NDDGQPGWPARPGSMGRPYPGHRVAVVDDEGRPCA-AGEDGEVAVCSTDVHGHPDPVFFL 419 Query: 388 MYWNNPEKTAATFMGE----WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVES 443 YW N + TA ++ W R+GD ++++GY Y GR+DD+ K SG + P E+E+ Sbjct: 420 GYWRNDDATAGKYLARDGLHWCRTGDLARIDEDGYLWYQGRADDVFKSSGYRIGPSEIEN 479 Query: 444 ALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGY----GAGEALRTDLKAHVKNLLAPY 499 L+ H AV AVV D + KAFIVL P A AL +L+ HV+ LAPY Sbjct: 480 CLLKHPAVSNCAVVPSPDPERGAVVKAFIVLVPSIVRSAQADAALVAELQQHVRGQLAPY 539 Query: 500 KYPRWIEFVDDLPKTATGKIQRFKLR 525 +YP+ IEF+ LP T TGKIQR LR Sbjct: 540 EYPKVIEFIAQLPMTTTGKIQRRVLR 565 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: 817 Number of extensions: 47 Number of successful extensions: 7 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: 577 Length adjustment: 36 Effective length of query: 491 Effective length of database: 541 Effective search space: 265631 Effective search space used: 265631 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