GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Sphingomonas koreensis DSMZ 15582

Best path

xylT, xdh, xylC, xad, kdaD, dopDH

Also see fitness data for the top candidates

Rules

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter Ga0059261_1891 Ga0059261_1777
xdh D-xylose dehydrogenase Ga0059261_1894 Ga0059261_2966
xylC xylonolactonase Ga0059261_1893
xad D-xylonate dehydratase Ga0059261_2649 Ga0059261_4216
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase Ga0059261_1895 Ga0059261_2636
dopDH 2,5-dioxopentanonate dehydrogenase Ga0059261_1896 Ga0059261_3374
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Ga0059261_3374 Ga0059261_1680
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Ga0059261_4049
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 Ga0059261_2293 Ga0059261_1321
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase Ga0059261_2675 Ga0059261_2792
Echvi_1871 sodium/xylose cotransporter Ga0059261_1623
gal2 galactose/glucose/xylose uniporter
glcB malate synthase Ga0059261_2979 Ga0059261_0896
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 Ga0059261_0562 Ga0059261_2293
gyaR glyoxylate reductase Ga0059261_1479 Ga0059261_2669
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase Ga0059261_2636 Ga0059261_1678
xdhA xylitol dehydrogenase Ga0059261_0846 Ga0059261_2605
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
xylG ABC transporter for xylose, ATP-binding component xylG
xylH ABC transporter for xylose, permease component xylH
xylK_Tm ABC transporter for xylose, ATP binding component xylK
xyrA xylitol reductase Ga0059261_0885 Ga0059261_3340

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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