GapMind for catabolism of small carbon sources


Definition of D-glucuronate catabolism

As rules and steps, or see full text


Overview: Glucuronate utilization in GapMind is based on MetaCyc pathways D-glucuronate degradation II (oxidation of 5-keto-4-deoxyglucarate, link), a related pathway via 5-keto-4-deoxyglucarate aldolase (link), or degradation via fructuronate (link). GapMind also includes a variation on the oxidative pathway with a glucarolactonase, as in Pseudomonas putida. MetaCyc pathway I (via L-gulonate and xylitol, link) is not reported in prokaryotes and is not described here.


exuT: D-glucuronate:H+ symporter ExuT

dctP: D-glucuronate TRAP transporter, solute receptor component

dctQ: D-glucuronate TRAP transporter, small permease component

dctM: D-glucuronate TRAP transporter, large permease component

kdgD: 5-dehydro-4-deoxyglucarate dehydratase

dopDH: 2,5-dioxopentanonate dehydrogenase

garL: 5-dehydro-4-deoxy-D-glucarate aldolase

garR: tartronate semialdehyde reductase

garK: glycerate 2-kinase

udh: D-glucuronate dehydrogenase

gci: D-glucaro-1,4-lactone cycloisomerase

uxuL: D-glucaro-1,5-lactonase UxuL or UxuF

gudD: D-glucarate dehydratase

uxaC: D-glucuronate isomerase

uxuB: D-mannonate dehydrogenase

uxuA: D-mannonate dehydratase

kdgK: 2-keto-3-deoxygluconate kinase

eda: 2-keto-3-deoxygluconate 6-phosphate aldolase



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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 (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:

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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