GapMind for catabolism of small carbon sources


D-glucuronate catabolism in Sinorhizobium meliloti 1021

Best path

dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH

Also see fitness data for the top candidates


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
dctP D-glucuronate TRAP transporter, solute receptor component SM_b21353 SM_b20036
dctQ D-glucuronate TRAP transporter, small permease component
dctM D-glucuronate TRAP transporter, large permease component SM_b21351 SMa0250
udh D-glucuronate dehydrogenase SMc04145
uxuL D-glucaro-1,5-lactonase UxuL or UxuF SMc04142 SMa0717
gudD D-glucarate dehydratase SMa0056
kdgD 5-dehydro-4-deoxyglucarate dehydratase SMa1440 SMc02404
dopDH 2,5-dioxopentanonate dehydrogenase SM_b20891 SM_b20262
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase SMc03153 SMc02043
exuT D-glucuronate:H+ symporter ExuT
garK glycerate 2-kinase SM_b20678 SMc04389
garL 5-dehydro-4-deoxy-D-glucarate aldolase SMc02778 SMc02404
garR tartronate semialdehyde reductase SM_b20679 SMa0237
gci D-glucaro-1,4-lactone cycloisomerase SMa1351 SM_b20510
kdgK 2-keto-3-deoxygluconate kinase SMc01531 SM_b21374
uxaC D-glucuronate isomerase SM_b21354
uxuA D-mannonate dehydratase SM_b20446 SM_b20510
uxuB D-mannonate dehydrogenase SM_b20749 SMc01501

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.



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 (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 paper from 2022 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