Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_011766777.1 AZO_RS15330 benzoate-CoA ligase family protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000061505.1:WP_011766777.1 Length = 532 Score = 226 bits (577), Expect = 1e-63 Identities = 163/505 (32%), Positives = 247/505 (48%), Gaps = 23/505 (4%) Query: 59 LIWRDINTGEEAKL---------SYHELSLMSNRVLSTLRKH-GLKKGDVVYLMTKVHPM 108 LI R++ G AKL SY EL+ NR S LR L++ D + + Sbjct: 28 LIGRNLAAGRGAKLAYIDDLGSYSYDELARRVNRCASALRGSLALRQEDRILMCVHDTVE 87 Query: 109 HWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLK-VE 167 VFL IK G + + T LT + +Y +D + + + + + LG + +E Sbjct: 88 FPTVFLGAIKAGVIPIAVNTLLTAHDYEYMLTDSRARIAVVSAALLPLFQPLLGKVPTLE 147 Query: 168 KFLIDGKRETWNS-----LEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSY- 221 + ++ G L+ S + T +D ++SG+TG PK +H S Sbjct: 148 RIVVAGTANPGPDSLAALLDTGSDQFDAAPTLADDACFWLYSSGSTGAPKGTVHIHSSLI 207 Query: 222 PVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYL 281 + ++G+ E D+ + + +A + PL VGAT V + + Sbjct: 208 QTAELYARPVIGINEGDVVFSAAKLFFAYGLGNGLTFPLAVGATAVLM--AERPTPAAVF 265 Query: 282 GEVENLGVTSFCAPPTAWRQFITLDLDQFRFE-RLRSVVSAGEPLNPEVIKIWKDKFNLT 340 + T F PT + + R E RLR+ SAGE L E+ K W ++F + Sbjct: 266 ERLRRHTPTIFYGVPTLYASMLASPECPTRAEMRLRACTSAGEALPEEIGKRWTERFGVD 325 Query: 341 IRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLN 400 I D G TE + + V+ G+ GKP P Y +RL+DDEGKEI+ P E G + + Sbjct: 326 ILDGIGSTEMLHIFLSNRAGNVRYGTTGKPVPGYAVRLIDDEGKEISAPGEPGELQIS-- 383 Query: 401 PRPIGLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFE 460 P +++ +K +F+ + +GDK D +GY+ + GR DD++K S V P E Sbjct: 384 -GPTAAAYYWNNREKTRNTFQGPWTRSGDKYQMDADGYYVYAGRSDDMLKVSGIYVSPIE 442 Query: 461 VESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYK 520 VESAL+ H AV EAAVVG D + KAYIVLK G + L +E++ +K+LL+PYK Sbjct: 443 VESALIAHEAVLEAAVVGCEDEDKLIKPKAYIVLKPGIAITDALRDELKAHVKSLLAPYK 502 Query: 521 VPRIIEFVDELPKTISGKIRRVELR 545 PR +EFV+ELPKT +GKI+R +LR Sbjct: 503 YPRWMEFVEELPKTATGKIQRFKLR 527 Lambda K H 0.318 0.137 0.402 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: 635 Number of extensions: 36 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: 564 Length of database: 532 Length adjustment: 36 Effective length of query: 528 Effective length of database: 496 Effective search space: 261888 Effective search space used: 261888 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 24 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