GapMind for catabolism of small carbon sources

 

Definition of D-gluconate catabolism

As rules and steps, or see full text

Rules

Overview: In most bacteria, gluconate degradation proceeds via D-gluconate 6-phosphate and either the Entner-Doudoroff pathway or the oxidative pentose phosphate pathway (link). Alternatively, gluconate can be oxidized in the periplasm to 2-ketogluconate before uptake (link).

Steps

gntA: gluconate TRAP transporter, small permease component

gntB: gluconate TRAP transporter, large permease component

gntC: gluconate TRAP transporter, periplasmic solute-binding component

gntEIIA: gluconate PTS system, IIA component

gntEIIB: gluconate PTS system, IIB component

gntEIIC: gluconate PTS system, IIC component

gntEIID: gluconate PTS system, IID component

gntT: gluconate:H+ symporter GntT

ght3: gluconate transporter Ght3

gntK: D-gluconate kinase

gnd: 6-phosphogluconate dehydrogenase, decarboxylating

edd: phosphogluconate dehydratase

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

gadh1: gluconate 2-dehydrogenase flavoprotein subunit

gadh2: gluconate 2-dehydrogenase cytochrome c subunit

gadh3: gluconate 2-dehydrogenase subunit 3

kguT: 2-ketogluconate transporter

kguK: 2-ketogluconokinase

kguD: 2-keto-6-phosphogluconate reductase

Links

Downloads

Related tools

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