D-galacturonate catabolism in Bradyrhizobium diazoefficiens USDA110

GapMind for catabolism of small carbon sources

D-galacturonate catabolism in Bradyrhizobium diazoefficiens USDA110

Best path

PS417_04205, udh, uxuL, garD, kdgD, dopDH

Rules

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.

all:

galacturonate-transport, uxaC, uxaB, uxaA, kdgK and eda
or galacturonate-transport, udh, gli, gci, kdgD and dopDH
or galacturonate-transport, udh, uxuL, garD, kdgD and dopDH
Comment: Pathway I begins with isomerization to tagaturonate (a keto sugar) by uxaC. Pathway II begins with oxidation to galactaro-1,5-lactone by udh, isomerization to the 1,4-lactone by gli, and isomerization to 5-keto-4-deoxyglucarate by gci. In another oxidative pathway, the 1,5-lactone is hydrolyzed by uxuL or uxuF giving meso-galactorate, and then a dehydratase (garD) forms 5-keto-4-deoxyglucarate. In both oxidative pathways, this is decarboxylated/dehydrated to 2,5-dioxopentanonate and oxidized to 2-oxoglutarate.

galacturonate-transport:

exuT
or gatA
or PS417_04205
Comment: Transporters were identified using query: transporter:galacturonate:D-galacturonate:galaturonate:D-galaturonate:D-galactopyranuronate:CPD-12523:CPD-12524:CPD-15633

15 steps (11 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
PS417_04205	D-galacturonate transporter	BJA_RS29705
udh	D-galacturonate dehydrogenase	BJA_RS13970
uxuL	D-galactaro-1,5-lactonase (UxuL or UxuF)	BJA_RS01845	BJA_RS17075
garD	meso-galactarate dehydratase (L-threo-forming) GarD	BJA_RS29730	BJA_RS14750
kdgD	5-dehydro-4-deoxyglucarate dehydratase	BJA_RS29715	BJA_RS25565
dopDH	2,5-dioxopentanonate dehydrogenase	BJA_RS29725	BJA_RS18690
Alternative steps:
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	BJA_RS19450	BJA_RS36950
exuT	D-galacturonate transporter ExuT
gatA	D-galacturonate transporter gatA
gci	D-galactarolactone cycloisomerase	BJA_RS33940	BJA_RS38680
gli	D-galactarolactone isomerase	BJA_RS11145	BJA_RS11120
kdgK	2-keto-3-deoxygluconate kinase	BJA_RS19445
uxaA	D-altronate dehydratase	BJA_RS14750	BJA_RS29730
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 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources