Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_043744440.1 AMB_RS12570 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000009985.1:WP_043744440.1 Length = 544 Score = 447 bits (1150), Expect = e-130 Identities = 231/532 (43%), Positives = 325/532 (61%), Gaps = 4/532 (0%) Query: 12 VDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSR 71 +D + Y LTPL FLER+ + D+ +VV+ D R+T+ YD SAL RG Sbjct: 11 LDKNPANYVPLTPLGFLERSASVYPDRISVVHGDLRFTWKQTYDRCRRLGSALAARGVGV 70 Query: 72 EDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLN 131 D ++ ++ N P E+ FGVP GGVL +N RL + +A+++ H ++K ++ D + Sbjct: 71 GDTVAVMAANTPAAYEAAFGVPMTGGVLCALNIRLDAEAIAFMLQHGEAKVLLTDREFAP 130 Query: 132 SLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMIT 191 ++ + ++A+ I+++ D +A T M Y + GG + + +E+ I Sbjct: 131 TIKKALSLLEAKPIVIDIDD--AAVTTGEMLGEMEYEAFIAGGDPEYAWVWPSDEWDAIA 188 Query: 192 LYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVA 251 L YTSGTTG PKGV++HHRGA++NA+ V+ M + VYLWTLPMFH W F W A Sbjct: 189 LNYTSGTTGNPKGVVYHHRGAYINALGNVVNWGMTGHPVYLWTLPMFHCNGWCFPWTLAA 248 Query: 252 VGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGA 311 + TNVCL +VD ++ +EK +VTHMC AP V L + +++ + V + A A Sbjct: 249 LAGTNVCLRRVDGGHMFAAIEKHKVTHMCGAPIVMGMLINAPEKDRRPLPHPVEFMTAAA 308 Query: 312 APAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVS 371 P A + ++ G + HVYGLTE YGP ++C W+ EWD LPL+E+AK+K+RQG+ YV+ Sbjct: 309 PPPAAVIGRLESQGFKITHVYGLTEVYGPATVCAWKEEWDELPLDERAKMKSRQGVRYVN 368 Query: 372 FE-MDVFD-ANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVV 429 E M V D + PVP DG T+GEV RG+ V GY KNP T E+F GWFH+GD V Sbjct: 369 EEAMMVADPVSLVPVPKDGATMGEVFYRGNVVMKGYLKNPSATNEAFSGGWFHTGDLGVW 428 Query: 430 HPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIE 489 H DGYIE+ DR KD+I +GGE +S+I VE L + P V AV PDEKWGE A I Sbjct: 429 HADGYIELKDRSKDIIISGGENISTIEVEGVLYQHPSVGEAAVVARPDEKWGETPCAFIG 488 Query: 490 LQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 L++G T EE++ FC+ERLAH++CP+ V F +P T+TGK+QKYVLR AK Sbjct: 489 LKDGATATAEEIMAFCRERLAHYKCPRTVVFTNLPKTSTGKVQKYVLREMAK 540 Lambda K H 0.319 0.136 0.411 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: 822 Number of extensions: 44 Number of successful extensions: 3 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: 549 Length of database: 544 Length adjustment: 36 Effective length of query: 513 Effective length of database: 508 Effective search space: 260604 Effective search space used: 260604 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