GapMind for catabolism of small carbon sources


D-glucuronate catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

exuT, uxaC, uxuB, uxuA, kdgK, eda


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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT
uxaC D-glucuronate isomerase
uxuB D-mannonate dehydrogenase CEV31_RS18355 CEV31_RS15260
uxuA D-mannonate dehydratase CEV31_RS18360
kdgK 2-keto-3-deoxygluconate kinase CEV31_RS10505 CEV31_RS16720
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CEV31_RS20745 CEV31_RS18545
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component CEV31_RS18370 CEV31_RS17950
dctP D-glucuronate TRAP transporter, solute receptor component CEV31_RS17960 CEV31_RS15460
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase CEV31_RS09240 CEV31_RS02995
garK glycerate 2-kinase CEV31_RS14540 CEV31_RS07550
garL 5-dehydro-4-deoxy-D-glucarate aldolase CEV31_RS10450 CEV31_RS09470
garR tartronate semialdehyde reductase CEV31_RS07545 CEV31_RS01040
gci D-glucaro-1,4-lactone cycloisomerase
gudD D-glucarate dehydratase
kdgD 5-dehydro-4-deoxyglucarate dehydratase CEV31_RS08840 CEV31_RS09470
udh D-glucuronate dehydrogenase CEV31_RS20180
uxuL D-glucaro-1,5-lactonase UxuL or UxuF CEV31_RS05370

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