Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_091295014.1 BLV57_RS31585 AMP-binding protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_900107045.1:WP_091295014.1 Length = 565 Score = 360 bits (923), Expect = e-103 Identities = 221/522 (42%), Positives = 302/522 (57%), Gaps = 25/522 (4%) Query: 38 FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97 FNW D F+ I + ++ AL R ++ ++Y ELS S+RV + LR+ G+ +G+ Sbjct: 36 FNWALDWFDAI--AQGNTRDAL--RIVDGASVTSVTYEELSRRSSRVANWLREQGVDRGN 91 Query: 98 VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157 V LM W LA +K G V++P+ T + A++ +D +S + + + Sbjct: 92 RVLLMLDNQAAVWETLLAAMKLGAVVIPTYTTIGPADL----ADRLERGAVSHVITTAAL 147 Query: 158 EEALGSLKVEKFLIDGKRETWNSLEDESSNAEPE-----DTRGEDVIINYFTSGTTGMPK 212 A + K ++ + W D +++A PE T + + YFTSGTT PK Sbjct: 148 TGAFAQADLTKIVVGPPVDGWLDYAD-AAHASPEFVPDGPTPADQELFLYFTSGTTSKPK 206 Query: 213 RVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGI-NY 271 H SYPVG ++ GV+ D+HLN+SA GWAK AWSSFF P ATV+ + N Sbjct: 207 LAQHNHTSYPVGHLSGMYWNGVQPGDVHLNISAPGWAKHAWSSFFVPFNAEATVLSVANP 266 Query: 272 EGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIK 331 G L + G T+FCAPPT WR I DL Q+ RLR S GEPLNPEVI+ Sbjct: 267 TGSAQV--VLDALVEHGATTFCAPPTVWRLLIQQDLRQWPV-RLREAGSVGEPLNPEVIE 323 Query: 332 IWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEIT-KPY 390 + + +T+RD +GQTETTA +GN L V+PGSMGKP P Y+I L+D IT +P Sbjct: 324 HVRQAWGITVRDAFGQTETTAQIGNTAGLPVRPGSMGKPLPGYEIVLIDP----ITGQPA 379 Query: 391 EVGHITVKLNPRPIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVI 449 + G I VKL+PRP+G+ GY + +KN E+F GYY+TGD A D +GY +VGR DDV Sbjct: 380 DEGEICVKLDPRPVGVMSGYLGNPEKNAETFGGGYYHTGDIASRDADGYLTYVGRADDVF 439 Query: 450 KTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIR 509 K+ DYRV PFE+ES LLEH VAEAAVV PD V + KA++ L G PS+ A I Sbjct: 440 KSYDYRVSPFELESVLLEHDEVAEAAVVPSPDVVGLVVPKAFVTLAAGAEPSESTARSIL 499 Query: 510 EKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEK 551 ++ L+P++ R +EF LPKT SGKIRR ELRK+E+ + Sbjct: 500 AHVQDQLAPHQWIRRLEF-GPLPKTTSGKIRRAELRKQEDAR 540 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: 771 Number of extensions: 39 Number of successful extensions: 5 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: 565 Length adjustment: 36 Effective length of query: 528 Effective length of database: 529 Effective search space: 279312 Effective search space used: 279312 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