Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF1060 HP15_1039 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Marino:GFF1060 Length = 542 Score = 430 bits (1106), Expect = e-125 Identities = 224/535 (41%), Positives = 328/535 (61%), Gaps = 5/535 (0%) Query: 10 EGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGF 69 +G+ P + Y+V +P+ F+ER + + AV++ RY ++ Y+ ASAL RG Sbjct: 7 QGLAPVDANYAVQSPVDFIERTATVYPEYPAVIHGAIRYNWAQTYERCRRLASALKGRGI 66 Query: 70 SREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY 129 R D ++ + N P +E+ FGVP G VL +N RL + +A++++H ++K V+ D + Sbjct: 67 GRGDTVAVMLPNIPAMVEAHFGVPMIGAVLNTLNVRLDAEAIAFMLDHGEAKVVIADREF 126 Query: 130 LNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSM 189 + + ++ + +++ D D+P E + + Y ++ G + E+ Sbjct: 127 GEVIRDAVSRLDTKPLVI-DVDDPEYGEGVQVS-DLDYEAFLQEGDPTFQWSFPENEWDA 184 Query: 190 ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWAT 249 I+L YTSGTTG PKGV++HHRGA++NA+ MD++ VYLWTLPMFH W F W Sbjct: 185 ISLNYTSGTTGNPKGVVYHHRGAYINAIGNQTVWSMDMHPVYLWTLPMFHCNGWCFPWTI 244 Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309 A+ T+VCL +VD I +L+ +VTHMC AP V L + + + V + A Sbjct: 245 TAMAGTHVCLRRVDPEKILQLIRDHQVTHMCGAPIVLNALLNVPESAKAGIDHDVKSMTA 304 Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY 369 GAAP + A++E+G + HVYGLTE YGP ++C W+ EWD+LPL ++A+ KARQG+ Y Sbjct: 305 GAAPPAQVIGAIEEMGIQVTHVYGLTEVYGPVTVCAWKSEWDALPLHDRARKKARQGVRY 364 Query: 370 VSFE-MDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAA 427 + V D N +PVP DGKTIGE+ +RG+ V GY KNP+ T E+FR GWFH+GD A Sbjct: 365 HTLAGTMVGDPNTMEPVPKDGKTIGEIFLRGNTVMKGYLKNPKATEEAFRGGWFHTGDLA 424 Query: 428 VVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTAR 487 V H DGY+EI DR KD+I +GGE +S+I VE TL P V AV PDEKWGE A Sbjct: 425 VWHEDGYMEIKDRLKDIIISGGENISTIEVEDTLYRHPAVLEAAVVARPDEKWGETPCAF 484 Query: 488 IELQ-EGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 + L+ E ++EE++I FC+E LA F+ PK + F +P T+TGK+QK+VLR++AK Sbjct: 485 VTLKPEAGDVSEEDIINFCREHLARFKVPKTIVFSELPKTSTGKIQKFVLRDQAK 539 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: 802 Number of extensions: 32 Number of successful extensions: 4 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: 542 Length adjustment: 35 Effective length of query: 514 Effective length of database: 507 Effective search space: 260598 Effective search space used: 260598 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