Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_011385057.1 AMB_RS13470 3-hydroxybutyrate dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000009985.1:WP_011385057.1 Length = 260 Score = 124 bits (312), Expect = 1e-33 Identities = 85/258 (32%), Positives = 127/258 (49%), Gaps = 13/258 (5%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDISK-THLEELASIAGVETHLL----- 61 L GK L+T + GIG A +GA V+ +E L + E + Sbjct: 2 LNGKRALVTGSTSGIGLGIARALAAQGASVMLNGFGDGAEIEALRAGLAKEFGVTVLYNG 61 Query: 62 -DVTDDDAIKALV----AKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHT 116 D++ D LV A++G VD+L N AG + E + WD +N ++F Sbjct: 62 ADLSKPDGAGVLVRDAEARLGGVDILVNNAGIQHVSPVEEFPLERWDAVIAINLTSVFQA 121 Query: 117 IRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRC 176 IRA LPGM A+ G I+N+ASA V V N+ AY ASK V+GLTK V + + C Sbjct: 122 IRAALPGMKARGWGRIINVASAHGLVASV-NKSAYVASKHGVLGLTKVVGLETAETDVTC 180 Query: 177 NAICPGTIESPSLNQRISTQAKETGKSEDEV-RAAFVARQPMGRIGKAEEVAALALYLAS 235 NAICPG + +P + ++I +A+ G ++ R +QP + E++ LA++L S Sbjct: 181 NAICPGWVLTPLVQKQIDARAEAQGVPVEQAGRDLLSEKQPSKKFTTPEQIGDLAVFLCS 240 Query: 236 DESNFTTGSIHMIDGGWS 253 TG+ +DGGW+ Sbjct: 241 GAGANMTGTSLTMDGGWT 258 Lambda K H 0.316 0.129 0.359 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: 146 Number of extensions: 5 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: 254 Length of database: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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