GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Ochrobactrum thiophenivorans DSM 7216

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF CEV31_RS02585 CEV31_RS17260
xylG ABC transporter for xylose, ATP-binding component xylG CEV31_RS02580 CEV31_RS17255
xylH ABC transporter for xylose, permease component xylH CEV31_RS02575 CEV31_RS17250
xylA xylose isomerase CEV31_RS17275
xylB xylulokinase CEV31_RS17270
Alternative steps:
aldA (glycol)aldehyde dehydrogenase CEV31_RS01730 CEV31_RS02995
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit CEV31_RS00175 CEV31_RS07500
aldox-small (glycol)aldehyde oxidoreductase, small subunit CEV31_RS00170 CEV31_RS07500
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 CEV31_RS20275 CEV31_RS17415
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase CEV31_RS09470
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase CEV31_RS06800 CEV31_RS18820
dopDH 2,5-dioxopentanonate dehydrogenase CEV31_RS09240 CEV31_RS02995
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase CEV31_RS03025
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA CEV31_RS09330
gtsB xylose ABC transporter, permease component 1 GtsB CEV31_RS09335 CEV31_RS14435
gtsC xylose ABC transporter, permease component 2 GtsC CEV31_RS09340 CEV31_RS07125
gtsD xylose ABC transporter, ATPase component GtsD CEV31_RS09345 CEV31_RS17415
gyaR glyoxylate reductase CEV31_RS05585 CEV31_RS02810
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase CEV31_RS06805 CEV31_RS17405
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase CEV31_RS14640
xad D-xylonate dehydratase CEV31_RS02600 CEV31_RS20170
xdh D-xylose dehydrogenase CEV31_RS05335 CEV31_RS13855
xdhA xylitol dehydrogenase CEV31_RS18365 CEV31_RS15265
xylC xylonolactonase CEV31_RS20185
xylE_Tm ABC transporter for xylose, substrate binding component xylE CEV31_RS09050
xylF_Tm ABC transporter for xylose, permease component xylF CEV31_RS09010 CEV31_RS20360
xylK_Tm ABC transporter for xylose, ATP binding component xylK CEV31_RS18890 CEV31_RS09015
xylT D-xylose transporter
xyrA xylitol reductase CEV31_RS19890

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