GapMind for catabolism of small carbon sources


Definition of D-ribose catabolism

As rules and steps, or see full text


Overview: Ribose degradation in GapMind is based on the MetaCyc pathway ribose phosphorylation (link), which yields the central metabolic intermediate D-ribofuranose 5-phosphate, or on uptake by a phosphotransferase system.


rbsA: D-ribose ABC transporter, ATPase component RbsA

rbsB: D-ribose ABC transporter, substrate-binding component RbsB

rbsC: D-ribose ABC transporter, permease component RbsC

frcA: D-ribose ABC transporter, ATPase component FrcA

frcB: D-ribose ABC transporter, substrate-binding component FrcB

frcC: D-ribose ABC transporter, permease component FrcC

fru2-IIA: D-ribose PTS, IIA component

fru2-IIB: D-ribose PTS, IIB component

fru2-IIC: D-ribose PTS, IIC component

rbsU: probable D-ribose transporter RbsU

BT2809: D-ribose transporter

LmGT2: D-ribose transporter LmGT2

PLT5: D-ribose transporter PLT5

rbsK: ribokinase



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 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