GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Halomonas xinjiangensis TRM 0175

Best path

gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA JH15_RS04285
gtsB xylose ABC transporter, permease component 1 GtsB JH15_RS04280
gtsC xylose ABC transporter, permease component 2 GtsC JH15_RS04275
gtsD xylose ABC transporter, ATPase component GtsD JH15_RS04270 JH15_RS03500
xdh D-xylose dehydrogenase JH15_RS09450 JH15_RS13090
xylC xylonolactonase JH15_RS06165 JH15_RS10355
xad D-xylonate dehydratase JH15_RS10360 JH15_RS10350
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase JH15_RS10285 JH15_RS15575
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase JH15_RS10280 JH15_RS07320
gyaR glyoxylate reductase JH15_RS14590 JH15_RS08520
glcB malate synthase JH15_RS12865
Alternative steps:
aldA (glycol)aldehyde dehydrogenase JH15_RS05310 JH15_RS15380
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit JH15_RS14180 JH15_RS00140
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 JH15_RS03500 JH15_RS04270
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase JH15_RS06535
dopDH 2,5-dioxopentanonate dehydrogenase JH15_RS10290 JH15_RS11595
Echvi_1871 sodium/xylose cotransporter JH15_RS04255
gal2 galactose/glucose/xylose uniporter
glcP glucose/mannose/xylose:H+ symporter
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase JH15_RS10230
xdhA xylitol dehydrogenase JH15_RS14530 JH15_RS10285
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 JH15_RS10185
xylG ABC transporter for xylose, ATP-binding component xylG JH15_RS10190 JH15_RS10340
xylH ABC transporter for xylose, permease component xylH JH15_RS10185 JH15_RS10345
xylK_Tm ABC transporter for xylose, ATP binding component xylK JH15_RS10190 JH15_RS10340
xylT D-xylose transporter
xyrA xylitol reductase JH15_RS14505 JH15_RS09395

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