GapMind for catabolism of small carbon sources


D-galacturonate catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

exuT, 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
exuT D-galacturonate transporter ExuT Pf1N1B4_5129 Pf1N1B4_2746
udh D-galacturonate dehydrogenase Pf1N1B4_4511 Pf1N1B4_2638
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) Pf1N1B4_4510 Pf1N1B4_413
garD meso-galactarate dehydratase (L-threo-forming) GarD Pf1N1B4_1107
kdgD 5-dehydro-4-deoxyglucarate dehydratase Pf1N1B4_1110 Pf1N1B4_3332
dopDH 2,5-dioxopentanonate dehydrogenase Pf1N1B4_1109 Pf1N1B4_4624
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Pf1N1B4_587 Pf1N1B4_399
gatA D-galacturonate transporter gatA
gci D-galactarolactone cycloisomerase Pf1N1B4_398 Pf1N1B4_5693
gli D-galactarolactone isomerase
kdgK 2-keto-3-deoxygluconate kinase Pf1N1B4_5638 Pf1N1B4_4765
PS417_04205 D-galacturonate transporter Pf1N1B4_1108 Pf1N1B4_397
uxaA D-altronate dehydratase Pf1N1B4_1107
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 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