GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Cronobacter condimenti 1330

Best path

xylF, xylG, xylH, xylA, xylB

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF BN137_RS01920
xylG ABC transporter for xylose, ATP-binding component xylG BN137_RS01915 BN137_RS06860
xylH ABC transporter for xylose, permease component xylH BN137_RS01910 BN137_RS17455
xylA xylose isomerase BN137_RS01925
xylB xylulokinase BN137_RS01930
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BN137_RS07600 BN137_RS09185
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit BN137_RS01840
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 BN137_RS10660 BN137_RS16695
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BN137_RS10075
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BN137_RS10485 BN137_RS07730
dopDH 2,5-dioxopentanonate dehydrogenase BN137_RS09185 BN137_RS06130
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase BN137_RS16425
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 BN137_RS16680
gtsD xylose ABC transporter, ATPase component GtsD BN137_RS16695 BN137_RS10660
gyaR glyoxylate reductase BN137_RS08125 BN137_RS02000
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase BN137_RS05280
xdh D-xylose dehydrogenase BN137_RS14795 BN137_RS07485
xdhA xylitol dehydrogenase BN137_RS02870 BN137_RS01705
xylC xylonolactonase BN137_RS00940
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF BN137_RS17455 BN137_RS04560
xylK_Tm ABC transporter for xylose, ATP binding component xylK BN137_RS14410 BN137_RS17460
xylT D-xylose transporter BN137_RS13235 BN137_RS02325
xyrA xylitol reductase BN137_RS04120 BN137_RS08340

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