Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_011385011.1 AMB_RS13240 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000009985.1:WP_011385011.1 Length = 541 Score = 419 bits (1076), Expect = e-121 Identities = 226/537 (42%), Positives = 314/537 (58%), Gaps = 12/537 (2%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G+D + + LTPL FLERA + D+ AV++ R T++ + A+AL RG Sbjct: 9 GLDRNAANFVALTPLTFLERAAAVWPDRLAVIHGPVRRTWAETFVRCRKLAAALTARGIG 68 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE--- 127 D ++ + N PE E+ FGVP G VL IN RL + +I+NH+++K ++ D Sbjct: 69 LGDTVALMGANTPETFEAHFGVPLTGAVLNAINTRLDADAITFILNHAEAKILITDREFS 128 Query: 128 PYLNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELV-KGGSRDPLPIPAKEE 186 P + L + +I ++DP K Y +L+ + S P +P +E Sbjct: 129 PVVKKALAALGRT-IPVIDIDDPQFKGGELLGEKN----YEQLLDEAASEAPWTLPT-DE 182 Query: 187 YSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFS 246 + I L YTSGTTG PKGV++HHRGA LNA++ L QM N+VYLWTLPMFH W F Sbjct: 183 WQAIALNYTSGTTGNPKGVVYHHRGAHLNAVSNALSWQMGDNTVYLWTLPMFHCNGWCFP 242 Query: 247 WATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHM 306 W V T+VCL V I + E+VT+ C AP V + + S+ V + Sbjct: 243 WTMAVVAGTSVCLRHVRVDAIMGAIRDEKVTNFCGAPIVLNMINNAPAALKEGISHAVKV 302 Query: 307 LVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQG 366 + AGAAP + M+ +G + HVYGLTE YGP C W +W+ L ++E+A++KARQG Sbjct: 303 MTAGAAPPAPVIAGMERMGWEVTHVYGLTECYGPTVQCVWHDKWNGLSIDEKAQIKARQG 362 Query: 367 I--PYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSG 424 + P + M + +P P DGKT+GE+ MRG+NV GY KN + T E+F GWFH+G Sbjct: 363 VRGPMLEGLMIADPISLEPAPKDGKTVGEIFMRGNNVMKGYLKNEKATEEAFAGGWFHTG 422 Query: 425 DAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVV 484 D AV HPDGYIEI DR KD+I +GGE +SSI VE L V AV PDEKWGE Sbjct: 423 DLAVCHPDGYIEIKDRSKDIIISGGENISSIEVEDILYAHLAVLEAAVVARPDEKWGETP 482 Query: 485 TARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 A I L++G + TE ++I FC+ER+AHF+ P+ + FG +P T+TGK+QK++LR +AK Sbjct: 483 CAFIALKDGAEATEADIITFCRERMAHFKVPRTIVFGGLPKTSTGKVQKFMLRQKAK 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: 757 Number of extensions: 38 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: 541 Length adjustment: 35 Effective length of query: 514 Effective length of database: 506 Effective search space: 260084 Effective search space used: 260084 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