Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate 5209735 Shew_2188 long-chain-fatty-acid--CoA ligase (RefSeq)
Query= SwissProt::Q8GQN9 (527 letters) >FitnessBrowser__PV4:5209735 Length = 557 Score = 167 bits (423), Expect = 9e-46 Identities = 148/550 (26%), Positives = 243/550 (44%), Gaps = 50/550 (9%) Query: 14 PAIKIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQ 73 PAI ++Y++ DL + +A + +++ + TY +L R + L+ L LQ Sbjct: 14 PAIIDAKQYSSLIDLF-ESSVAKYADQPAFVNMGATLTYRKLEERSRAFAAYLQNELKLQ 72 Query: 74 PKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELL 133 DRV + + + + +P G ++ G+V + +N L T + ++ L DS A+ VV Sbjct: 73 KGDRVAIMMPNLLQYPIALFGILRAGMVVVNVNPLYTPRELKHQLNDSGAKAIVVVSNFA 132 Query: 134 PLFAPMLGKVPTLEHLVVAGGAGE-----------------------------DSLAALL 164 ++ + P V+ G G+ S+ L Sbjct: 133 NTLEQVVEQTPVKS--VILTGLGDLLSAPKRTLVNFVVKYIKKMVPKYHLPHAISMRQSL 190 Query: 165 ATGSEQFEAAPT-RPDDHCFWLYSSGSTGAPKGTVHIHSDLIHT---AELYARPILGIRE 220 + G PT + DD F Y+ G+TG KG + H +++ A+ P+L + Sbjct: 191 SKGRRLQYVKPTIKGDDIAFLQYTGGTTGVSKGAMLTHGNIVSNLLQADAAYSPLLADGK 250 Query: 221 GDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAE-RPTPAAVFERLRRHQPDIFYGVPT 279 + V +A L+ + L + L GA +L+ R PA V E L++H GV T Sbjct: 251 -EFVVTALPLYHIFALTVNCLLFLHKGANNLLITNPRDIPAFVSE-LKKHPFTALTGVNT 308 Query: 280 LYASMLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTE---MLHI 336 L+ +++++ + L+ G A+ V +WQ +L+G G TE +L Sbjct: 309 LFNALVSSEEFKTLDFSNLKLSIGGGMAVQRAVADKWQGITKTRLLEGYGLTEASPLLTC 368 Query: 337 FLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKT 396 N G + G+ G PV +++ DE+G + G GEL GP YW PE+T Sbjct: 369 CPYNLEG--YNGSIGFPVANTDMQVRDEEG-NVLPQGETGELFAKGPQVMKGYWQRPEET 425 Query: 397 AATFMGE-WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAA 455 A + + +GD ++++G++ R DM+ VSG V P EVE + H VLE A Sbjct: 426 AKVIDKDGYLATGDIGYMDEQGFFFIVDRKKDMILVSGFNVFPNEVEEVVALHPKVLEVA 485 Query: 456 VVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTA 515 VG E K F+V K + H ++ L YK P+ +EF D+LPK+ Sbjct: 486 AVGVPHEVSGELVKVFVVPKD----KSLTEEQVIKHCRHHLTGYKIPKLVEFRDELPKSN 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: 653 Number of extensions: 37 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