GapMind for catabolism of small carbon sources


D-xylose catabolism in Sinorhizobium meliloti 1021

Best path

xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF SM_b20895 SM_b20902
xylG ABC transporter for xylose, ATP-binding component xylG SM_b20894 SM_b20713
xylH ABC transporter for xylose, permease component xylH SM_b20893 SM_b20352
xdh D-xylose dehydrogenase SMc04133 SMc00880
xylC xylonolactonase SMa0717 SMa0060
xad D-xylonate dehydratase SMa0235 SM_b20890
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase SM_b21111 SMc01635
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase SM_b21112 SMc04240
gyaR glyoxylate reductase SMc02849 SMc01943
glcB malate synthase SMc02581
Alternative steps:
aldA (glycol)aldehyde dehydrogenase SMc02780 SM_b21185
aldox-large (glycol)aldehyde oxidoreductase, large subunit SMc03102 SM_b20132
aldox-med (glycol)aldehyde oxidoreductase, medium subunit SMc03103 SM_b20130
aldox-small (glycol)aldehyde oxidoreductase, small subunit SMc03101 SM_b20131
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter SM_b20632
araV component of Arabinose, fructose, xylose porter SM_b20235 SMc03065
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase SMc02404 SM_b20299
dopDH 2,5-dioxopentanonate dehydrogenase SM_b20891 SM_b20262
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA SMc04396 SMc04259
gtsB xylose ABC transporter, permease component 1 GtsB SMc04395 SMc04258
gtsC xylose ABC transporter, permease component 2 GtsC SMc04394 SMc04257
gtsD xylose ABC transporter, ATPase component GtsD SMc04393 SM_b21216
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase SMa0247
xdhA xylitol dehydrogenase SMc01992 SMa0512
xylA xylose isomerase SMc03163
xylB xylulokinase SMc03164 SMc02341
xylE_Tm ABC transporter for xylose, substrate binding component xylE SMc03813 SMc03165
xylF_Tm ABC transporter for xylose, permease component xylF SM_b20352 SMc02772
xylK_Tm ABC transporter for xylose, ATP binding component xylK SM_b20713 SMc02337
xylT D-xylose transporter
xyrA xylitol reductase SM_b20500 SMa0563

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