GapMind for catabolism of small carbon sources


Definition of D-glucuronate catabolism

As text, or see rules and steps

# Glucuronate utilization in GapMind is based on MetaCyc pathways
# D-glucuronate degradation II (oxidation of 5-keto-4-deoxyglucarate, metacyc:PWY-6501),
# a related pathway via 5-keto-4-deoxyglucarate aldolase (metacyc:PWY-6516),
# or degradation via fructuronate (metacyc:PWY-7247).
# GapMind also includes a variation on the oxidative pathway with a glucarolactonase, as in Pseudomonas putida.
# MetaCyc pathway I (via L-gulonate and xylitol, metacyc:PWY-5525) is not reported in prokaryotes
# and is not described here.

exuT	D-glucuronate:H+ symporter ExuT	curated:SwissProt::P0AA78	curated:TCDB::P0AA78	curated:TCDB::P94774

# Transporters were identified using
# query: transporter:glucuronate:D-glucuronate:D-glucopyranuronate:CPD-14488:CPD-12521:CPD-15530
glucuronate-transport: exuT

# Genetic data from Pseudomonas putida suggests the involvement of a TRAP transporter:
# dctP-like PP_1169 (Q88NN8),
# dctQ-like PP_1168 (Q88NN9),
# and dctM-like PP_1167 (Q88NP0).
# Furthermore, PP_1169 is nearly identical to Pput_1203, which binds D-glucuronate
# (see PMC4310620 and PDB:4xfeA).
# The related substrate-binding proteins Bpro_3107 (Q128M1) and Bamb_6123 (Q0B2F6)
# was also shown to bind D-glucuronate (and D-galacturonate).
dctP	D-glucuronate TRAP transporter, solute receptor component	uniprot:Q88NN8	curated:SwissProt::Q128M1	curated:SwissProt::Q0B2F6
dctQ	D-glucuronate TRAP transporter, small permease component	uniprot:Q88NN9
dctM	D-glucuronate TRAP transporter, large permease component	uniprot:Q88NP0
glucuronate-transport: dctP dctQ dctM

# Porin OdpF was ignored

# 5-dehydro-4-deoxyglucarate is an intermediate in glucuronate catabolism.

import galacturonate.steps:kdgD # 5-dehydro-4-deoxyglucarate dehydratase
import xylose.steps:dopDH # 2,5-dioxopentanonate dehydrogenase

# As part of pathway II, 5-dehydro-4-deoxyglucarate is dehydrated/decarboxylated to
# 2,5-dioxopentanoate (by kdgD) and oxidized to 2-oxoglutarate (by dopDH).
5-dehydro-4-deoxyglucarate-degradation: kdgD dopDH

garL	5-dehydro-4-deoxy-D-glucarate aldolase	EC:

# glxR (G6278-MONOMER) is linked to this reaction (but not this EC) in ecocyc and metacyc.
# PGA1_c14880 (Phaeo:GFF1469) had been reannotated as a tartronate semialdehyde reductase but
# this is questionable.
garR	tartronate semialdehyde reductase	EC:	curated:ecocyc::G6278-MONOMER	ignore:reanno::Phaeo:GFF1469

import deoxyribonate.steps:garK # glycerate 2-kinase

# Alternatively, 5-dehydro-4-deoxy-D-glucarate can be consumed by aldolase garL,
# which forms pyruvate and tartronate semialdehyde (2-hydroxy-3-oxopropionate);
# tartronate semialdehyde is reduced to D-glycerate and phosphorylated
# to enter glycolysis.
5-dehydro-4-deoxyglucarate-degradation: garL garR garK

udh	D-glucuronate dehydrogenase	EC:
gci	D-glucaro-1,4-lactone cycloisomerase	EC:

# In pathway II, dehydrogenase udh forms D-glucaro-1,5-lactone, which spontaneously rearranges to
# D-glucaro-1,4-lactone, and the cycloisomerase gci forms 5-dehydro-4-deoxy-D-glucarate.
all: glucuronate-transport udh gci 5-dehydro-4-deoxyglucarate-degradation

# Biochemical studies showed that lactonases uxuL and uxuF act on
# D-glucaro-1,5-lactone (PMC6304669). These include
# Rpic_4446 = B2UIY8,
# PSPTO_1052 = Q888H2,
# Bcep1808_2255 = A4JG52,
# BMULJ_02167 = A0A0H3KPX2,
# Bcep18194_A5499 = Q39EM3,
# and PSPTO_2765 = Q881W7,
# Genetic data from P. putida KT2440
# shows that a uxuL-like protein (PP_1170 = Q88NN7) is involved in glucuronate
# utilization. UxuL/uxuF are also active on galactaro-1,5-lactone,
# and PS417_17365 from WCS417 may well act on both substrates, but this is not proven.
uxuL	D-glucaro-1,5-lactonase UxuL or UxuF	uniprot:B2UIY8	uniprot:Q888H2	uniprot:A4JG52	uniprot:A0A0H3KPX2	uniprot:Q39EM3	uniprot:Q881W7	uniprot:Q88NN7	ignore:reanno::WCS417:GFF3393

gudD	D-glucarate dehydratase	EC:

# In P. putida, genetic data suggests that the lactone is hydrolyzed
# to D-glucarate by uxuL and the dehydratase gudD forms 5-dehydro-4-deoxy-D-glucarate.
all: glucuronate-transport udh uxuL gudD 5-dehydro-4-deoxyglucarate-degradation

uxaC	D-glucuronate isomerase	EC:
# uxuB is D-mannonate oxidoreductase
# uxuA is D-mannonate dehydratase
import myoinositol.steps:uxuB uxuA
import glucosamine.steps:kdgK # 2-keto-3-deoxygluconate kinase
import glucose.steps:eda # 2-keto-3-deoxygluconate 6-phosphate aldolase

# In the fructuronate pathway, an isomerase (uxaC) converts D-glucuronate to D-fructuronate,
# followed by oxidation to D-mannonate, dehydration to
# 2-dehydro-3-deoxy-D-gluconate, phosphorylation to
# 2-dehydro-3-deoxy-D-gluconate 6-phosphate, and an aldolase reaction
# to glyceraldehyde-3-phosphate and pyruvate.
all: glucuronate-transport uxaC uxuB uxuA kdgK eda



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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:

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