GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Bacteroides thetaiotaomicron VPI-5482

Best path

xylT, xylA, xylB

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter BT0794 BT4397
xylA xylose isomerase BT0793
xylB xylulokinase BT0792 BT4423
Alternative steps:
aldA (glycol)aldehyde dehydrogenase
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit
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 BT1291 BT1751
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BT0895
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BT3771 BT1911
dopDH 2,5-dioxopentanonate dehydrogenase
Echvi_1871 sodium/xylose cotransporter BT0355
gal2 galactose/glucose/xylose uniporter BT4397
glcB malate synthase
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 BT1291 BT1751
gyaR glyoxylate reductase BT1207 BT1575
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BT3883
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase BT2078
xdh D-xylose dehydrogenase BT3232 BT1911
xdhA xylitol dehydrogenase BT3771 BT1911
xylC xylonolactonase
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 BT1383

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, 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