GapMind for catabolism of small carbon sources


Definition of D-xylose catabolism

As rules and steps, or see full text


Overview: Xylose degradation in GapMind is based on MetaCyc pathways I via D-xylulose (link), II via xylitol (link), III or V via 2-dehydro-3-deoxy-D-arabinonate (DKDP) dehydratase (link, link), IV via DKDP aldolase (link), as well as another pathway via DKDP dehydrogenase (PMC6336799).


xylT: D-xylose transporter

gal2: galactose/glucose/xylose uniporter

glcP: glucose/mannose/xylose:H+ symporter

Echvi_1871: sodium/xylose cotransporter

xylF: ABC transporter for xylose, substrate binding component xylF

xylG: ABC transporter for xylose, ATP-binding component xylG

xylH: ABC transporter for xylose, permease component xylH

xylF_Tm: ABC transporter for xylose, permease component xylF

xylE_Tm: ABC transporter for xylose, substrate binding component xylE

xylK_Tm: ABC transporter for xylose, ATP binding component xylK

araV: component of Arabinose, fructose, xylose porter

araU: component of Arabinose, fructose, xylose porter

araT: component of Arabinose, fructose, xylose porter

araS: component of Arabinose, fructose, xylose porter

gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA

gtsB: xylose ABC transporter, permease component 1 GtsB

gtsC: xylose ABC transporter, permease component 2 GtsC

gtsD: xylose ABC transporter, ATPase component GtsD

xylA: xylose isomerase

xylB: xylulokinase

xyrA: xylitol reductase

xdhA: xylitol dehydrogenase

xdh: D-xylose dehydrogenase

xylC: xylonolactonase

xad: D-xylonate dehydratase

kdaD: 2-keto-3-deoxy-D-arabinonate dehydratase

dopDH: 2,5-dioxopentanonate dehydrogenase

DKDP-aldolase: 2-dehydro-3-deoxy-D-arabinonate aldolase

aldox-large: (glycol)aldehyde oxidoreductase, large subunit

aldox-med: (glycol)aldehyde oxidoreductase, medium subunit

aldox-small: (glycol)aldehyde oxidoreductase, small subunit

aldA: (glycol)aldehyde dehydrogenase

gyaR: glyoxylate reductase

glcB: malate synthase

DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase

HDOP-hydrol: 5-hydroxy-2,4-dioxopentanonate hydrolase



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