Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_086511178.1 BZY95_RS17500 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_002151265.1:WP_086511178.1 Length = 543 Score = 419 bits (1076), Expect = e-121 Identities = 220/523 (42%), Positives = 320/523 (61%), Gaps = 4/523 (0%) Query: 22 LTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRN 81 L+PL F+ER+ + D AV++ D R ++ + ASAL +RG + ++ + N Sbjct: 20 LSPLTFIERSASIYPDYPAVIHGDIRRSWRETWARCRRLASALEKRGIKPGETVAAMLPN 79 Query: 82 RPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIK 141 P E+ FGVP AG VL +N RL + +AY++ H +++ V+VD + + + ++ Sbjct: 80 VPAMFEAHFGVPLAGCVLNTLNIRLDAEAIAYMLEHGEAQAVLVDPEFAGVIEDAVSRLA 139 Query: 142 AEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGL 201 + ++++ D ET R + Y L+ G + ++E+ I+L YTSGTTG Sbjct: 140 IKPLVIDVDDALYEGET-RHIGELEYEALLAEGDPEYAYQLPEDEWQAISLNYTSGTTGK 198 Query: 202 PKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDK 261 PKGV++HHRGA+LNA++ +LE M + VYLWTLPMFH W F W A +VCL + Sbjct: 199 PKGVVYHHRGAYLNAVSNILEWAMPHHPVYLWTLPMFHCNGWCFPWTIAANAGVSVCLRR 258 Query: 262 VDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAM 321 VD I L+ E+VTH AP V L + F + V + AGAAP + + + Sbjct: 259 VDPKKIMDLIVDEKVTHFSGAPIVLNGLVNLPAEQKRAFDHPVKVTTAGAAPPASVIAGV 318 Query: 322 QEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFE-MDVFDAN 380 +++G + HVYGLTE YGP ++C WR WD LPLEE+A++KARQG+ Y E + V D N Sbjct: 319 EKLGIEVTHVYGLTEVYGPVTVCAWREAWDELPLEERARIKARQGVRYHMLEALCVADPN 378 Query: 381 G-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVD 439 +PVP DG+TIGE++MRG+NV GY KN T ++ GW+H+GD AV HPDGYIEI D Sbjct: 379 TLEPVPKDGETIGEILMRGNNVMKGYLKNEAATEQALEGGWYHTGDLAVWHPDGYIEIKD 438 Query: 440 RFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGV-KLTE 498 R KD+I +GGE +S+I VE + P V+ AV PDEKWGE A ++L+ G ++TE Sbjct: 439 RSKDIIISGGENISTIEVEDAIYSHPAVEEAAVVAKPDEKWGETPCAFVKLKVGYGEVTE 498 Query: 499 EEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 ++I+ C++ LA F+ PK V F +P T+TGK+QK+VLR EA+ Sbjct: 499 ADIIEHCRQHLARFKVPKTVIFTELPKTSTGKIQKFVLREEAR 541 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: 780 Number of extensions: 39 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: 543 Length adjustment: 35 Effective length of query: 514 Effective length of database: 508 Effective search space: 261112 Effective search space used: 261112 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 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