GapMind for catabolism of small carbon sources


D-xylose catabolism in Caulobacter crescentus NA1000

Best path

xylT, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter CCNA_00857
xdh D-xylose dehydrogenase CCNA_00864 CCNA_01283
xylC xylonolactonase CCNA_00863 CCNA_01882
xad D-xylonate dehydratase CCNA_00862 CCNA_01488
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase CCNA_00866
dopDH 2,5-dioxopentanonate dehydrogenase CCNA_00865 CCNA_02881
Alternative steps:
aldA (glycol)aldehyde dehydrogenase CCNA_03242 CCNA_00424
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit CCNA_00022 CCNA_02353
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter
araV component of Arabinose, fructose, xylose porter CCNA_03235 CCNA_01670
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase CCNA_01253
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase CCNA_03495 CCNA_00092
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase CCNA_01843
glcP glucose/mannose/xylose:H+ symporter
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 CCNA_03235 CCNA_01670
gyaR glyoxylate reductase CCNA_03838 CCNA_03322
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase
xdhA xylitol dehydrogenase CCNA_03124 CCNA_03495
xylA xylose isomerase
xylB xylulokinase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF
xylF_Tm ABC transporter for xylose, permease component xylF CCNA_00904
xylG ABC transporter for xylose, ATP-binding component xylG CCNA_00903
xylH ABC transporter for xylose, permease component xylH CCNA_00904
xylK_Tm ABC transporter for xylose, ATP binding component xylK CCNA_00903
xyrA xylitol reductase CCNA_03541 CCNA_03097

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:

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