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:

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