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



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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