GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Novosphingobium barchaimii LL02

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter V474_RS08805
xdh D-xylose dehydrogenase V474_RS08800 V474_RS20390
xylC xylonolactonase V474_RS23735 V474_RS08205
xad D-xylonate dehydratase V474_RS08210 V474_RS23740
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase V474_RS08795
dopDH 2,5-dioxopentanonate dehydrogenase V474_RS22325 V474_RS23760
Alternative steps:
aldA (glycol)aldehyde dehydrogenase V474_RS17175 V474_RS19995
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit V474_RS22880
aldox-small (glycol)aldehyde oxidoreductase, small subunit V474_RS22800 V474_RS19730
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 V474_RS07795 V474_RS07990
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase V474_RS20490
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase V474_RS01415 V474_RS20170
Echvi_1871 sodium/xylose cotransporter V474_RS08170
gal2 galactose/glucose/xylose uniporter
glcB malate synthase V474_RS01360
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 V474_RS07795 V474_RS15950
gyaR glyoxylate reductase V474_RS02970 V474_RS00340
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase V474_RS24045 V474_RS15385
xdhA xylitol dehydrogenase V474_RS24695 V474_RS19410
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 V474_RS07525

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.

Links

Downloads

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:

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