GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Cupriavidus basilensis 4G11

Best path

xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

Also see fitness data for the top candidates

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF
xylG ABC transporter for xylose, ATP-binding component xylG RR42_RS32900 RR42_RS03360
xylH ABC transporter for xylose, permease component xylH RR42_RS03365 RR42_RS32890
xdh D-xylose dehydrogenase RR42_RS30145 RR42_RS19270
xylC xylonolactonase RR42_RS30140 RR42_RS33665
xad D-xylonate dehydratase RR42_RS18585 RR42_RS33950
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase RR42_RS34980 RR42_RS23420
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase RR42_RS00385 RR42_RS05150
gyaR glyoxylate reductase RR42_RS14190 RR42_RS33330
glcB malate synthase RR42_RS12175 RR42_RS24325
Alternative steps:
aldA (glycol)aldehyde dehydrogenase RR42_RS11330 RR42_RS21760
aldox-large (glycol)aldehyde oxidoreductase, large subunit RR42_RS02365 RR42_RS26495
aldox-med (glycol)aldehyde oxidoreductase, medium subunit RR42_RS13625 RR42_RS26500
aldox-small (glycol)aldehyde oxidoreductase, small subunit RR42_RS02370 RR42_RS13620
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 RR42_RS18590 RR42_RS22875
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase RR42_RS06250 RR42_RS36370
dopDH 2,5-dioxopentanonate dehydrogenase RR42_RS23090 RR42_RS04830
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
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 RR42_RS12955 RR42_RS18590
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xdhA xylitol dehydrogenase RR42_RS35005 RR42_RS22860
xylA xylose isomerase
xylB xylulokinase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF RR42_RS03365 RR42_RS32890
xylK_Tm ABC transporter for xylose, ATP binding component xylK RR42_RS32900 RR42_RS03360
xylT D-xylose transporter
xyrA xylitol reductase RR42_RS20325 RR42_RS35195

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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