Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate 201721 SO2581 long-chain-fatty-acid--CoA ligase (NCBI ptt file)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__MR1:201721 Length = 557 Score = 165 bits (417), Expect = 5e-45 Identities = 144/550 (26%), Positives = 242/550 (44%), Gaps = 45/550 (8%) Query: 11 NTPPAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTL 70 + P I + ++Y++ D+ +A + +I+ + TY +L R + L+ L Sbjct: 12 DVPAEINV-DQYSSLIDMF-ETAVAKYADQPAFINMGATLTYRKLEERSRAFAAYLQNEL 69 Query: 71 GLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ 130 LQ DRV + + + + +P G ++ G+V + +N L T + ++ L DS A+ VV Sbjct: 70 KLQKGDRVALMMPNLLQYPIALFGILRAGMVVVNVNPLYTPRELKHQLIDSGAKAIVVVS 129 Query: 131 ELLPLFAPMLGKVPTLEHLVVAGGAGED-----------------------------SLA 161 ++ + P V+ G G+ S+ Sbjct: 130 NFARTLEEVVDQTPVKS--VIITGLGDLLSAPKRTLVNFVVKYIKKLVPKYDLPHALSMR 187 Query: 162 ALLATGSEQFEAAPT-RPDDHCFWLYSSGSTGAPKGTVHIHSDLI-HTAELYARPILGIR 219 L+ G P DD F Y+ G+TG KG + HS+++ + + +R Sbjct: 188 ETLSRGRRMQYVKPVITGDDLAFLQYTGGTTGVSKGAMLTHSNVVANVLQANGAYSPALR 247 Query: 220 EG-DVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAE-RPTPAAVFERLRRHQPDIFYGV 277 +G + V +A L+ + L + L G+ +L+ R P V E L+++ GV Sbjct: 248 DGSEFVVTALPLYHIFALTVNCLLFLHKGSQNLLITNPRDIPGFVAE-LKKYPFTALTGV 306 Query: 278 PTLYASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIF 337 TL+ +++ + D + RL+ G A+ + V +WQ +L+G G TE + Sbjct: 307 NTLFNALVNSSDFSELDFSRLKLSIGGGMAVQKAVADKWQNITKTRLLEGYGLTEASPLL 366 Query: 338 LSNRAG-DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKT 396 D + G+ G P P +++ D+ G + G GEL GP YW PE+T Sbjct: 367 TCCPYNLDGYNGSIGFPAPSTLIQVRDDAG-NVLPQGETGELFGKGPQIMKGYWQRPEET 425 Query: 397 AATFMGE-WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAA 455 A + W +GD ++++G++ R DM+ VSG V P EVE + H V+E A Sbjct: 426 AKVIDNDGWLATGDIGYMDEQGFFYIVDRKKDMILVSGFNVFPNEVEEVVALHPKVIEVA 485 Query: 456 VVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTA 515 VG ++ K F+V K E D+ H + L YK P+ +EF D+LPKT Sbjct: 486 AVGVPNDASGELVKVFVVKKDKSLTAE----DIIKHCRVHLTGYKVPKLVEFRDELPKTN 541 Query: 516 TGKIQRFKLR 525 GKI R +LR Sbjct: 542 VGKILRRELR 551 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: 675 Number of extensions: 40 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: 557 Length adjustment: 35 Effective length of query: 492 Effective length of database: 522 Effective search space: 256824 Effective search space used: 256824 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