GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Rhodococcus qingshengii djl-6-2

Best path

xylT, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter C1M55_RS14300
xylA xylose isomerase
xylB xylulokinase C1M55_RS22535
Alternative steps:
aldA (glycol)aldehyde dehydrogenase C1M55_RS02975 C1M55_RS22335
aldox-large (glycol)aldehyde oxidoreductase, large subunit C1M55_RS30095
aldox-med (glycol)aldehyde oxidoreductase, medium subunit C1M55_RS30105
aldox-small (glycol)aldehyde oxidoreductase, small subunit C1M55_RS30100 C1M55_RS16880
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter C1M55_RS20465
araV component of Arabinose, fructose, xylose porter C1M55_RS18505 C1M55_RS30235
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase C1M55_RS04705
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase C1M55_RS23600 C1M55_RS25840
dopDH 2,5-dioxopentanonate dehydrogenase C1M55_RS28050 C1M55_RS22335
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter C1M55_RS14300
glcB malate synthase C1M55_RS16050 C1M55_RS20480
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 C1M55_RS30235 C1M55_RS20455
gyaR glyoxylate reductase C1M55_RS12520 C1M55_RS23785
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase C1M55_RS12530
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase C1M55_RS25540 C1M55_RS12495
xdh D-xylose dehydrogenase C1M55_RS10245 C1M55_RS10280
xdhA xylitol dehydrogenase C1M55_RS18180 C1M55_RS01525
xylC xylonolactonase
xylE_Tm ABC transporter for xylose, substrate binding component xylE C1M55_RS10300
xylF ABC transporter for xylose, substrate binding component xylF
xylF_Tm ABC transporter for xylose, permease component xylF C1M55_RS26585 C1M55_RS10270
xylG ABC transporter for xylose, ATP-binding component xylG C1M55_RS10275
xylH ABC transporter for xylose, permease component xylH C1M55_RS26585
xylK_Tm ABC transporter for xylose, ATP binding component xylK C1M55_RS10275
xyrA xylitol reductase C1M55_RS04335 C1M55_RS10645

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