Definition of D-galacturonate catabolism

GapMind for catabolism of small carbon sources

Definition of D-galacturonate catabolism

# Galacturonate utilization in GapMind is based on MetaCyc pathways
# D-galacturonate degradation I via tagaturonate (metacyc:GALACTUROCAT-PWY),
# pathway II via oxidation to 5-dehydro-4-deoxy-glucarate (metacyc:PWY-6486),
# and another oxidative pathway (PMID:30249705).
# Pathway III via galactonate (metacyc:PWY-6491) is reported only in fungi
# and is not included in GapMind.


# BT4105 (Q8A0B6), CA265_RS19855 (A0A1X9Z948), Pf1N1B4_5129 (A0A166QG26), and HSERO_RS23010 (D8IX31) are related
# proteins with specific phenotypes on D-galacturonate
exuT	D-galacturonate transporter ExuT	curated:SwissProt::P0AA78	curated:TCDB::P0AA78	curated:TCDB::P94774	uniprot:Q8A0B6	uniprot:A0A1X9Z948	uniprot:A0A166QG26	uniprot:D8IX31

# Transporters were identified using
# query: transporter:galacturonate:D-galacturonate:galaturonate:D-galaturonate:D-galactopyranuronate:CPD-12523:CPD-12524:CPD-15633
galacturonate-transport: exuT

gatA	D-galacturonate transporter gatA	curated:TCDB::A2R3H2
galacturonate-transport: gatA

PS417_04205	D-galacturonate transporter	curated:reanno::WCS417:GFF828
galacturonate-transport: PS417_04205


uxaC	D-galacturonate isomerase	EC:5.3.1.12
uxaB	tagaturonate reductase	EC:1.1.1.58
uxaA	D-altronate dehydratase	EC:4.2.1.7
# 2-keto-3-deoxygluconate kinase and 2-keto-3-deoxygluconate 6-phosphate aldolase
import glucosamine.steps:kdgK
import glucose.steps:eda

# Pathway I begins with isomerization to 
# tagaturonate (a keto sugar) by uxaC.
all: galacturonate-transport uxaC uxaB uxaA kdgK eda

udh	D-galacturonate dehydrogenase	EC:1.1.1.203
gli	D-galactarolactone isomerase	EC:5.4.1.4
# BRENDA misannotates gli as gci
gci	D-galactarolactone cycloisomerase	EC:5.5.1.27	ignore:BRENDA::A9CEQ7
kdgD	5-dehydro-4-deoxyglucarate dehydratase	EC:4.2.1.41
import xylose.steps:dopDH # 2,5-dioxopentanonate dehydrogenase

# 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.
all: galacturonate-transport udh gli gci kdgD dopDH

# Two families of D-galactaro-1,5-lactonase were described, uxuL and uxuF.
# All of these proteins are active on D-glucaro-1,5-lactone as well,
# although PSPTO_2765 is much more active on galactaro,1-5-lactone.
# UxuL = Rpic_4446 PSPTO_1052
# UxuF = Bcep1808_2255 BMULJ_02167 Bcep18194_A5499 PSPTO_2765
# PS417_17365 (GFF3393) and HSERO_RS15795 were inferred from mutant phenotype
uxuL	D-galactaro-1,5-lactonase (UxuL or UxuF)	uniprot:B2UIY8	uniprot:Q888H2	uniprot:A4JG52	uniprot:A0A0H3KPX2	uniprot:Q39EM3	uniprot:Q881W7	curated:reanno::WCS417:GFF3393	curated:reanno::HerbieS:HSERO_RS15795

# Q8EMJ9 is the D-threo-forming enzyme, and is misannotated in BRENDA
garD	meso-galactarate dehydratase (L-threo-forming) GarD	EC:4.2.1.42	ignore:BRENDA::Q8EMJ9

# 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.
all: galacturonate-transport udh uxuL garD kdgD dopDH

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

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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