GapMind for catabolism of small carbon sources

 

Definition of D-galacturonate catabolism

As rules and steps, or see full text

Rules

Overview: Galacturonate utilization in GapMind is based on MetaCyc pathways D-galacturonate degradation I via tagaturonate (link), pathway II via oxidation to 5-dehydro-4-deoxy-glucarate (link), and another oxidative pathway (PMID:30249705). Pathway III via galactonate (link) is reported only in fungi and is not included in GapMind.

Steps

exuT: D-galacturonate transporter ExuT

gatA: D-galacturonate transporter gatA

PS417_04205: D-galacturonate transporter

uxaC: D-galacturonate isomerase

uxaB: tagaturonate reductase

uxaA: D-altronate dehydratase

kdgK: 2-keto-3-deoxygluconate kinase

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

udh: D-galacturonate dehydrogenase

gli: D-galactarolactone isomerase

gci: D-galactarolactone cycloisomerase

kdgD: 5-dehydro-4-deoxyglucarate dehydratase

dopDH: 2,5-dioxopentanonate dehydrogenase

uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF)

garD: meso-galactarate dehydratase (L-threo-forming) GarD

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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