GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Duganella sacchari Sac-22

Best path

xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH

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
xylF ABC transporter for xylose, substrate binding component xylF BUA36_RS11795
xylG ABC transporter for xylose, ATP-binding component xylG BUA36_RS11790 BUA36_RS13070
xylH ABC transporter for xylose, permease component xylH BUA36_RS11785 BUA36_RS29215
xdh D-xylose dehydrogenase BUA36_RS13995 BUA36_RS17920
xylC xylonolactonase BUA36_RS22905 BUA36_RS03365
xad D-xylonate dehydratase BUA36_RS03355 BUA36_RS22860
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
dopDH 2,5-dioxopentanonate dehydrogenase BUA36_RS17085 BUA36_RS13655
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BUA36_RS07090 BUA36_RS13005
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit BUA36_RS16595 BUA36_RS19880
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 BUA36_RS02205 BUA36_RS22420
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase BUA36_RS02945 BUA36_RS16015
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BUA36_RS17920 BUA36_RS10905
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase BUA36_RS28060
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA BUA36_RS21485 BUA36_RS02065
gtsB xylose ABC transporter, permease component 1 GtsB BUA36_RS21480
gtsC xylose ABC transporter, permease component 2 GtsC BUA36_RS21475
gtsD xylose ABC transporter, ATPase component GtsD BUA36_RS21470 BUA36_RS20915
gyaR glyoxylate reductase BUA36_RS05860 BUA36_RS24285
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BUA36_RS15740 BUA36_RS24810
xdhA xylitol dehydrogenase BUA36_RS06610 BUA36_RS22870
xylA xylose isomerase
xylB xylulokinase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF BUA36_RS29215 BUA36_RS11785
xylK_Tm ABC transporter for xylose, ATP binding component xylK BUA36_RS11790 BUA36_RS23405
xylT D-xylose transporter BUA36_RS18045
xyrA xylitol reductase BUA36_RS26810 BUA36_RS07845

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