GapMind for catabolism of small carbon sources


D-galacturonate catabolism in Pseudomonas fluorescens GW456-L13

Best path

PS417_04205, udh, uxuL, garD, kdgD, dopDH

Also see fitness data for the top candidates


Overview: Galacturonate utilization in GapMind is based on MetaCyc pathways D-galacturonate degradation I via tagaturonate (link), pathway II via oxidation to 5-dehydro-4-deoxy-glucarate (link), and another oxidative pathway (PMID:30249705). Pathway III via galactonate (link) is reported only in fungi and is not included in GapMind.

15 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_04205 D-galacturonate transporter PfGW456L13_5043 PfGW456L13_3476
udh D-galacturonate dehydrogenase PfGW456L13_1301
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) PfGW456L13_2118
garD meso-galactarate dehydratase (L-threo-forming) GarD PfGW456L13_5042 PfGW456L13_3478
kdgD 5-dehydro-4-deoxyglucarate dehydratase PfGW456L13_5045 PfGW456L13_4507
dopDH 2,5-dioxopentanonate dehydrogenase PfGW456L13_5044 PfGW456L13_3316
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PfGW456L13_1903 PfGW456L13_2127
exuT D-galacturonate transporter ExuT PfGW456L13_1423 PfGW456L13_2130
gatA D-galacturonate transporter gatA
gci D-galactarolactone cycloisomerase PfGW456L13_2128 PfGW456L13_3930
gli D-galactarolactone isomerase
kdgK 2-keto-3-deoxygluconate kinase PfGW456L13_2869 PfGW456L13_2950
uxaA D-altronate dehydratase PfGW456L13_3478 PfGW456L13_5042
uxaB tagaturonate reductase
uxaC D-galacturonate isomerase

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:

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