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:

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