GapMind for catabolism of small carbon sources


D-xylose catabolism in Acidovorax sp. GW101-3H11

Best path

xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH

Also see fitness data for the top candidates


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).

36 steps (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF Ac3H11_610
xylG ABC transporter for xylose, ATP-binding component xylG Ac3H11_609 Ac3H11_2881
xylH ABC transporter for xylose, permease component xylH Ac3H11_608 Ac3H11_1841
xdh D-xylose dehydrogenase Ac3H11_614 Ac3H11_2257
xylC xylonolactonase Ac3H11_615 Ac3H11_2081
xad D-xylonate dehydratase Ac3H11_3523 Ac3H11_604
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase Ac3H11_3522
dopDH 2,5-dioxopentanonate dehydrogenase Ac3H11_612 Ac3H11_255
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Ac3H11_1480 Ac3H11_1496
aldox-large (glycol)aldehyde oxidoreductase, large subunit Ac3H11_3591
aldox-med (glycol)aldehyde oxidoreductase, medium subunit Ac3H11_3592
aldox-small (glycol)aldehyde oxidoreductase, small subunit Ac3H11_3590 Ac3H11_3428
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter Ac3H11_2065
araV component of Arabinose, fructose, xylose porter Ac3H11_4785 Ac3H11_2941
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase Ac3H11_277 Ac3H11_1501
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase Ac3H11_360 Ac3H11_2257
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase Ac3H11_4835
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA Ac3H11_2062
gtsB xylose ABC transporter, permease component 1 GtsB Ac3H11_2064
gtsC xylose ABC transporter, permease component 2 GtsC Ac3H11_2065
gtsD xylose ABC transporter, ATPase component GtsD Ac3H11_2066 Ac3H11_4785
gyaR glyoxylate reductase Ac3H11_2599 Ac3H11_2341
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase Ac3H11_4136 Ac3H11_1487
xdhA xylitol dehydrogenase Ac3H11_2257 Ac3H11_1922
xylA xylose isomerase
xylB xylulokinase Ac3H11_2937
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF Ac3H11_2880 Ac3H11_3036
xylK_Tm ABC transporter for xylose, ATP binding component xylK Ac3H11_609 Ac3H11_2881
xylT D-xylose transporter
xyrA xylitol reductase Ac3H11_4133

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



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