Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_016554064.1 RGCCGE502_RS10110 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000298315.2:WP_016554064.1 Length = 362 Score = 148 bits (373), Expect = 4e-40 Identities = 115/373 (30%), Positives = 194/373 (52%), Gaps = 36/373 (9%) Query: 194 YTSGTTGLPKGVMHHHRGAFLNAMA-EVLEHQMDLNSVYLWTLP------------MFHA 240 YT+G+TGLPKG ++ H GAFL ++ + +D ++ +L T+P +FHA Sbjct: 4 YTTGSTGLPKGAVYPH-GAFLQSILYTAMLEGIDPSTRWLHTMPAAGVPLMHMIRNLFHA 62 Query: 241 ASWGFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLAD--YMKRNNL 298 A ATV VG + + L L+ +E T++ PT+ +L + ++R ++ Sbjct: 63 A------ATVIVGPWSA-----EQALF--LIGREHTTNVVLVPTMLNSLLESSMLERTDM 109 Query: 299 KFSNRVHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQ 358 S R+ A + P KAM+ ++G TE G S+ + + + L + + Sbjct: 110 S-SMRLFGYGASSLPPKTIKKAMKAFDRPFLQMFGTTELMGM-SMMLFPSDHE-LGITTR 166 Query: 359 AKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRD 418 ++ G P ++ V D +G+ +P G+T GE+++R GY+ PEK+AE +D Sbjct: 167 PEILGSAGKPLPFVDVKVVDGDGRSLP-SGET-GELIVRSDTQFSGYWNAPEKSAEVIKD 224 Query: 419 GWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDE 478 GW ++GD A GY+ + DR K I +GG V VE L E P + VAV G PDE Sbjct: 225 GWIYTGDLASRDEAGYVYLSDRAKFRIRSGGYDVFPTEVENALAEHPAISEVAVIGLPDE 284 Query: 479 KWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVE-FGPIPMTATGKMQK-YVL 536 ++GE + A + G +T +E+ +FC+ ++A F+ PK ++ + IP TGK+QK ++ Sbjct: 285 RYGERIHAVVTTVPGKTVTSDELREFCRNKIAAFKVPKRIDIWTEIPKGPTGKIQKRAII 344 Query: 537 RNEAKAKANKEKS 549 + A A+++ S Sbjct: 345 EHFASEAASRQAS 357 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: 448 Number of extensions: 21 Number of successful extensions: 2 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: 362 Length adjustment: 32 Effective length of query: 517 Effective length of database: 330 Effective search space: 170610 Effective search space used: 170610 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: 51 (24.3 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