Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate PP_4549 PP_4549 long-chain-fatty-acid/CoA ligase
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__Putida:PP_4549 Length = 565 Score = 176 bits (447), Expect = 2e-48 Identities = 145/508 (28%), Positives = 224/508 (44%), Gaps = 39/508 (7%) Query: 51 TYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLT 110 TY EL + L+ L+P DR+ V + + + +P GA++ G++ + N L T Sbjct: 51 TYGELYALSGAFAAWLQQHTDLKPGDRIAVQLPNVLQYPVAVFGAMRAGLIVVNTNPLYT 110 Query: 111 ESDYEYMLTDSAARVAVVSQELLPLFAPMLGK--------------VPTLEHLVVAG--- 153 + E+ DS A+ V + L ++ K +P L+ L++ Sbjct: 111 AREMEHQFNDSGAKALVCLANMAHLAEKVVPKTQVRHVIVTEVADLLPPLKRLLINSVIK 170 Query: 154 ------------GAGEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIH 201 A + A L G EA P + +D Y+ G+TG KG + H Sbjct: 171 YVKKMVPAYNLPQAVRFNDALALGKGQPVTEANP-QANDVAVLQYTGGTTGVAKGAMLTH 229 Query: 202 SDLIHTAELYARPILG--IREG-DVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPT 258 +L+ L R ++G + EG +++ + L+ Y + + +G VL++ Sbjct: 230 RNLVANM-LQCRALMGSNLHEGCEILITPLPLYHIYAFTFHCMAMMLIGNHNVLISNPRD 288 Query: 259 PAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQA 318 A+ + L + + F G+ TL+ ++ N L+ S G AL V RW+A Sbjct: 289 LPAMVKELGKWKFSGFVGLNTLFVALCNNEAFRALDFSALKITLSGGMALQLSVAERWKA 348 Query: 319 RFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGEL 378 G I +G G TE + N + GT G PVP ++ID+ G E+ G GEL Sbjct: 349 VTGCAICEGYGMTETSPVAAVNPSEANQVGTIGIPVPSTLCKVIDDAGNELPL-GEVGEL 407 Query: 379 QISGPSSAVMYWNNPEKTAATFMGE-WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVS 437 + GP YW + TA E W ++GD ++ +GY R DM+ VSG V Sbjct: 408 CVKGPQVMKGYWQREDATAEILDSEGWLKTGDIAVIQADGYMRIVDRKKDMILVSGFNVY 467 Query: 438 PIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLA 497 P E+E L A VL+ A +G DE K FIV+KPG + + H++ + Sbjct: 468 PNELEDVLAALPGVLQCAAIGVPDEKSGEVIKVFIVVKPGM---TVTKEQVMEHMRANVT 524 Query: 498 PYKYPRWIEFVDDLPKTATGKIQRFKLR 525 YK PR IEF D LP T GKI R +LR Sbjct: 525 GYKVPRHIEFRDSLPTTNVGKILRRELR 552 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: 721 Number of extensions: 37 Number of successful extensions: 6 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: 565 Length adjustment: 35 Effective length of query: 492 Effective length of database: 530 Effective search space: 260760 Effective search space used: 260760 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