GapMind for catabolism of small carbon sources

 

Finding step srlD for D-sorbitol (glucitol) catabolism in Marinobacter adhaerens HP15

5 candidates for srlD: sorbitol 6-phosphate 2-dehydrogenase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo HP15_2361 3-oxoacyl-(acyl carrier protein) reductase Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 30% 97% 129.8 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 45% 190.3
lo HP15_2784 3-ketoacyl-(acyl-carrier-protein) reductase sorbitol-6-phosphate dehydrogenase (characterized) 32% 99% 114.8 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 51% 239.6
lo HP15_2724 short-chain dehydrogenase/reductase SDR Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 32% 98% 111.3 S-1-(4-hydroxyphenyl)-ethanol dehydrogenase 40% 184.9
lo HP15_880 oxidoreductase, short chain dehydrogenase/reductase family sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized) 35% 95% 102.1 17-beta-hydroxysteroid dehydrogenase 14; 17-beta-HSD 14; 17-beta-hydroxysteroid dehydrogenase DHRS10; Dehydrogenase/reductase SDR family member 10; Retinal short-chain dehydrogenase/reductase retSDR3; Short chain dehydrogenase/reductase family 47C member 1; EC 1.1.1.- 40% 158.7
lo HP15_1007 3-hydroxyacyl-CoA dehydrogenase type II Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 34% 80% 89.4 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) 56% 264.6

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step srlD

Or cluster all characterized srlD proteins

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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