GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Belnapia rosea CPCC 100156

Best path

xylT, xdh, xylC, xad, kdaD, dopDH

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xdh D-xylose dehydrogenase BLR02_RS11585 BLR02_RS13095
xylC xylonolactonase BLR02_RS16110 BLR02_RS27415
xad D-xylonate dehydratase BLR02_RS09825 BLR02_RS21720
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase BLR02_RS21320
dopDH 2,5-dioxopentanonate dehydrogenase BLR02_RS18460 BLR02_RS07320
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BLR02_RS07320 BLR02_RS18460
aldox-large (glycol)aldehyde oxidoreductase, large subunit BLR02_RS08385 BLR02_RS04845
aldox-med (glycol)aldehyde oxidoreductase, medium subunit BLR02_RS08390 BLR02_RS10255
aldox-small (glycol)aldehyde oxidoreductase, small subunit BLR02_RS08380 BLR02_RS02250
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 BLR02_RS07875 BLR02_RS15665
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BLR02_RS02000
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BLR02_RS09815 BLR02_RS11620
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase BLR02_RS00220
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 BLR02_RS15660
gtsD xylose ABC transporter, ATPase component GtsD BLR02_RS07875 BLR02_RS15665
gyaR glyoxylate reductase BLR02_RS09805 BLR02_RS07845
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BLR02_RS09810 BLR02_RS25525
xdhA xylitol dehydrogenase BLR02_RS02430 BLR02_RS15010
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 BLR02_RS06615
xyrA xylitol reductase BLR02_RS23585 BLR02_RS04335

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 24 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