GapMind for catabolism of small carbon sources


D-xylose catabolism in Klebsiella michiganensis M5al

Best path

xylF, xylG, xylH, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF BWI76_RS27030
xylG ABC transporter for xylose, ATP-binding component xylG BWI76_RS27035 BWI76_RS07240
xylH ABC transporter for xylose, permease component xylH BWI76_RS27040 BWI76_RS14865
xylA xylose isomerase BWI76_RS27025
xylB xylulokinase BWI76_RS27020 BWI76_RS19340
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BWI76_RS13210 BWI76_RS05620
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit BWI76_RS17570
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 BWI76_RS06035 BWI76_RS03270
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BWI76_RS26315 BWI76_RS03425
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BWI76_RS11090 BWI76_RS13720
dopDH 2,5-dioxopentanonate dehydrogenase BWI76_RS05620 BWI76_RS07615
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase BWI76_RS01660
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB xylose ABC transporter, permease component 1 GtsB BWI76_RS23380
gtsC xylose ABC transporter, permease component 2 GtsC BWI76_RS06705
gtsD xylose ABC transporter, ATPase component GtsD BWI76_RS17830 BWI76_RS06690
gyaR glyoxylate reductase BWI76_RS26960 BWI76_RS27925
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BWI76_RS03870 BWI76_RS05690
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase BWI76_RS18100 BWI76_RS27935
xdh D-xylose dehydrogenase BWI76_RS16755 BWI76_RS08900
xdhA xylitol dehydrogenase BWI76_RS11545 BWI76_RS11535
xylC xylonolactonase BWI76_RS21470 BWI76_RS23720
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF BWI76_RS14865 BWI76_RS00280
xylK_Tm ABC transporter for xylose, ATP binding component xylK BWI76_RS07240 BWI76_RS00275
xylT D-xylose transporter BWI76_RS23425 BWI76_RS24055
xyrA xylitol reductase BWI76_RS24305 BWI76_RS11560

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