GapMind for catabolism of small carbon sources


D-xylose catabolism in Dinoroseobacter shibae DFL-12

Best path

xylT, xylA, xylB

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xylA xylose isomerase Dshi_1996
xylB xylulokinase Dshi_1997 Dshi_1235
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Dshi_2887 Dshi_1425
aldox-large (glycol)aldehyde oxidoreductase, large subunit Dshi_2659 Dshi_4202
aldox-med (glycol)aldehyde oxidoreductase, medium subunit Dshi_1210 Dshi_4200
aldox-small (glycol)aldehyde oxidoreductase, small subunit Dshi_1211 Dshi_2660
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 Dshi_2017 Dshi_3141
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase Dshi_0149
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase Dshi_0553 Dshi_2182
dopDH 2,5-dioxopentanonate dehydrogenase Dshi_0577 Dshi_2442
Echvi_1871 sodium/xylose cotransporter Dshi_3906 Dshi_3904
gal2 galactose/glucose/xylose uniporter
glcB malate synthase Dshi_1227 Dshi_2874
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 Dshi_1246 Dshi_1650
gtsD xylose ABC transporter, ATPase component GtsD Dshi_1416 Dshi_2017
gyaR glyoxylate reductase Dshi_2970 Dshi_2643
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase Dshi_2542 Dshi_0967
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase Dshi_2542
xad D-xylonate dehydratase Dshi_1244 Dshi_0129
xdh D-xylose dehydrogenase Dshi_1243 Dshi_3712
xdhA xylitol dehydrogenase Dshi_0551 Dshi_4159
xylC xylonolactonase Dshi_1240
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF Dshi_2000
xylF_Tm ABC transporter for xylose, permease component xylF Dshi_2432 Dshi_2431
xylG ABC transporter for xylose, ATP-binding component xylG Dshi_2433 Dshi_0530
xylH ABC transporter for xylose, permease component xylH Dshi_2431 Dshi_1999
xylK_Tm ABC transporter for xylose, ATP binding component xylK Dshi_2433 Dshi_0530
xyrA xylitol reductase Dshi_0539

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.



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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