GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Rhodobacter johrii JA192

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xylA xylose isomerase C8J29_RS16920
xylB xylulokinase C8J29_RS16915
Alternative steps:
aldA (glycol)aldehyde dehydrogenase C8J29_RS18670 C8J29_RS02515
aldox-large (glycol)aldehyde oxidoreductase, large subunit C8J29_RS06015
aldox-med (glycol)aldehyde oxidoreductase, medium subunit C8J29_RS06010
aldox-small (glycol)aldehyde oxidoreductase, small subunit C8J29_RS06020 C8J29_RS13785
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 C8J29_RS18185 C8J29_RS18590
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase C8J29_RS18900 C8J29_RS11255
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase C8J29_RS21165 C8J29_RS07510
dopDH 2,5-dioxopentanonate dehydrogenase C8J29_RS18180 C8J29_RS20275
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase C8J29_RS01715 C8J29_RS11720
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB xylose ABC transporter, permease component 1 GtsB C8J29_RS14165
gtsC xylose ABC transporter, permease component 2 GtsC C8J29_RS05980
gtsD xylose ABC transporter, ATPase component GtsD C8J29_RS18660 C8J29_RS18185
gyaR glyoxylate reductase C8J29_RS03220 C8J29_RS14545
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase C8J29_RS07505 C8J29_RS21530
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase C8J29_RS07520 C8J29_RS18010
xdh D-xylose dehydrogenase C8J29_RS15950 C8J29_RS20320
xdhA xylitol dehydrogenase C8J29_RS17990 C8J29_RS18470
xylC xylonolactonase C8J29_RS13445
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF C8J29_RS16900 C8J29_RS17285
xylF_Tm ABC transporter for xylose, permease component xylF C8J29_RS16565 C8J29_RS17225
xylG ABC transporter for xylose, ATP-binding component xylG C8J29_RS16570 C8J29_RS15005
xylH ABC transporter for xylose, permease component xylH C8J29_RS16905 C8J29_RS17295
xylK_Tm ABC transporter for xylose, ATP binding component xylK C8J29_RS03430 C8J29_RS16570
xyrA xylitol reductase C8J29_RS03225 C8J29_RS13770

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