Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate Pf6N2E2_2872 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2872 Length = 563 Score = 173 bits (438), Expect = 2e-47 Identities = 143/511 (27%), Positives = 225/511 (44%), Gaps = 45/511 (8%) Query: 51 TYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLT 110 TY EL + L+ LQP DR+ V + + + +P GAI+ G++ + N L T Sbjct: 51 TYGELYELSGAFAAYLQQHTDLQPGDRIAVQLPNVLQYPVAVFGAIRAGLIVVNTNPLYT 110 Query: 111 ESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAAL------- 163 + E+ DS A+ V + L ++ K +++H++V A D L L Sbjct: 111 AREMEHQFNDSGAKALVCLANMAHLAEAVVPKT-SVKHVIVTEVA--DLLPPLKRLLINS 167 Query: 164 -----------------------LATGSEQ--FEAAPTRPDDHCFWLYSSGSTGAPKGTV 198 L+ G +Q EA PT DD Y+ G+TG KG + Sbjct: 168 VIKYVKKMVPAYHLPKAVKFNDVLSKGHDQPVSEANPTS-DDVAVLQYTGGTTGVAKGAM 226 Query: 199 HIHSDLIHTAELYARPILG--IREG-DVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAE 255 H +L+ L + ++G + EG +++ + L+ Y + + +G +L++ Sbjct: 227 LTHRNLVANM-LQCKALMGSNLNEGCEILITPLPLYHIYAFTFHCMAMMLIGNHNILISN 285 Query: 256 RPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPEDVGRR 315 A+ + L + + F G+ TL+ ++ N K L+ S G AL R Sbjct: 286 PRDLPAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSALKVTLSGGMALQLAAAER 345 Query: 316 WQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVA 375 W+A G I +G G TE + N ++ GT G PVP ++I++ G E G Sbjct: 346 WKAVTGCPICEGYGMTETSPVATVNPIQNIQIGTIGIPVPSTLCKVINDAGVE-QPLGEI 404 Query: 376 GELQISGPSSAVMYWNNPEKTAATFMGE-WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGI 434 GEL + GP YW + T E W ++GD L+ +GY R DM+ +SG Sbjct: 405 GELCVKGPQVMKGYWQRQDATDEILDSEGWLKTGDIALIQPDGYMRIVDRKKDMILISGF 464 Query: 435 YVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKN 494 V P E+E L VL+ A +G DE K FIV +PG + + H++ Sbjct: 465 NVYPNELEDVLATLPGVLQCAAIGIPDEKSGEAIKIFIVARPGV---TLTKEQVMEHMRA 521 Query: 495 LLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525 + YK P+ +EF D LP T GKI R +LR Sbjct: 522 NVTGYKVPKAVEFRDALPTTNVGKILRRELR 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: 689 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 527 Length of database: 563 Length adjustment: 35 Effective length of query: 492 Effective length of database: 528 Effective search space: 259776 Effective search space used: 259776 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