Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_011385057.1 AMB_RS13470 3-hydroxybutyrate dehydrogenase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_000009985.1:WP_011385057.1 Length = 260 Score = 142 bits (357), Expect = 9e-39 Identities = 93/263 (35%), Positives = 138/263 (52%), Gaps = 27/263 (10%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLA-GKPVEARKLDVRDDAAIK 63 L GK AL+T + GIGL A A +GA V+ ++G G +EA + + + + Sbjct: 2 LNGKRALVTGSTSGIGLGIARALAAQGASVM-----LNGFGDGAEIEALRAGLAKEFGVT 56 Query: 64 AL-------------------AAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVK 104 L A +G VD+L N AG H + E E WD +N+ Sbjct: 57 VLYNGADLSKPDGAGVLVRDAEARLGGVDILVNNAGIQHVSPVEEFPLERWDAVIAINLT 116 Query: 105 AMYRMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFIT 164 ++++ IRA LP M +G G IIN++SA V V N+ AY ASK V+GLTK V + Sbjct: 117 SVFQAIRAALPGMKARGWGRIINVASAHGLVASV-NKSAYVASKHGVLGLTKVVGLETAE 175 Query: 165 RGVRCNAICPGTVASPSLEQRIVAQAQAQGATLD-AVQAAFVARQPMGRIGKPEEIAALA 223 V CNAICPG V +P ++++I A+A+AQG ++ A + +QP + PE+I LA Sbjct: 176 TDVTCNAICPGWVLTPLVQKQIDARAEAQGVPVEQAGRDLLSEKQPSKKFTTPEQIGDLA 235 Query: 224 LYLGSDESSFTTGHAHVIDGGWS 246 ++L S + TG + +DGGW+ Sbjct: 236 VFLCSGAGANMTGTSLTMDGGWT 258 Lambda K H 0.320 0.133 0.381 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: 160 Number of extensions: 9 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: 247 Length of database: 260 Length adjustment: 24 Effective length of query: 223 Effective length of database: 236 Effective search space: 52628 Effective search space used: 52628 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 (21.8 bits) S2: 46 (22.3 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