GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Escherichia coli BW25113

Best path

exuT, uxaC, uxuB, uxuA, kdgK, eda

Also see fitness data for the top candidates

Rules

Overview: Glucuronate utilization in GapMind is based on MetaCyc pathways D-glucuronate degradation II (oxidation of 5-keto-4-deoxyglucarate, link), a related pathway via 5-keto-4-deoxyglucarate aldolase (link), or degradation via fructuronate (link). GapMind also includes a variation on the oxidative pathway with a glucarolactonase, as in Pseudomonas putida. MetaCyc pathway I (via L-gulonate and xylitol, link) is not reported in prokaryotes and is not described here.

18 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT b3093
uxaC D-glucuronate isomerase b3092
uxuB D-mannonate dehydrogenase b4323 b2172
uxuA D-mannonate dehydratase b4322 b1581
kdgK 2-keto-3-deoxygluconate kinase b3526
eda 2-keto-3-deoxygluconate 6-phosphate aldolase b1850 b4477
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component b3578
dctP D-glucuronate TRAP transporter, solute receptor component b3579
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase b2661 b0312
garK glycerate 2-kinase b3124 b0514
garL 5-dehydro-4-deoxy-D-glucarate aldolase b0268 b3126
garR tartronate semialdehyde reductase b0509 b3125
gci D-glucaro-1,4-lactone cycloisomerase b4478
gudD D-glucarate dehydratase b2787 b2788
kdgD 5-dehydro-4-deoxyglucarate dehydratase b0268
udh D-glucuronate dehydrogenase
uxuL D-glucaro-1,5-lactonase UxuL or UxuF b0767

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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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