GapMind for catabolism of small carbon sources


D-glucuronate catabolism in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_487 Pf6N2E2_1301
dctQ D-glucuronate TRAP transporter, small permease component Pf6N2E2_486
dctM D-glucuronate TRAP transporter, large permease component Pf6N2E2_485 Pf6N2E2_1302
udh D-glucuronate dehydrogenase Pf6N2E2_489 Pf6N2E2_4908
uxuL D-glucaro-1,5-lactonase UxuL or UxuF Pf6N2E2_488 Pf6N2E2_5966
gudD D-glucarate dehydratase Pf6N2E2_2116 Pf6N2E2_692
kdgD 5-dehydro-4-deoxyglucarate dehydratase Pf6N2E2_3299 Pf6N2E2_2747
dopDH 2,5-dioxopentanonate dehydrogenase Pf6N2E2_612 Pf6N2E2_3298
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf6N2E2_2883 Pf6N2E2_5976
exuT D-glucuronate:H+ symporter ExuT
garK glycerate 2-kinase Pf6N2E2_5836 Pf6N2E2_460
garL 5-dehydro-4-deoxy-D-glucarate aldolase Pf6N2E2_1103 Pf6N2E2_1314
garR tartronate semialdehyde reductase Pf6N2E2_5837 Pf6N2E2_1929
gci D-glucaro-1,4-lactone cycloisomerase Pf6N2E2_5977 Pf6N2E2_1104
kdgK 2-keto-3-deoxygluconate kinase Pf6N2E2_2046 Pf6N2E2_629
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase Pf6N2E2_5977
uxuB D-mannonate dehydrogenase Pf6N2E2_806

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