GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Chromobacterium vaccinii MWU205

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xylA xylose isomerase
xylB xylulokinase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase VL52_RS20940 VL52_RS07105
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit VL52_RS19360
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter VL52_RS08415
araV component of Arabinose, fructose, xylose porter VL52_RS13280 VL52_RS18065
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase VL52_RS02940 VL52_RS20160
dopDH 2,5-dioxopentanonate dehydrogenase VL52_RS09525 VL52_RS20020
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase VL52_RS03490
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 VL52_RS12740 VL52_RS04920
gyaR glyoxylate reductase VL52_RS16495 VL52_RS02475
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase VL52_RS14235
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase VL52_RS11430 VL52_RS05510
xdh D-xylose dehydrogenase VL52_RS17095 VL52_RS02940
xdhA xylitol dehydrogenase VL52_RS13400 VL52_RS17095
xylC xylonolactonase
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 VL52_RS18720
xylG ABC transporter for xylose, ATP-binding component xylG VL52_RS18715 VL52_RS07675
xylH ABC transporter for xylose, permease component xylH VL52_RS18720
xylK_Tm ABC transporter for xylose, ATP binding component xylK VL52_RS18715 VL52_RS07675
xyrA xylitol reductase VL52_RS13810 VL52_RS19845

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