Definition of D-gluconate catabolism

GapMind for catabolism of small carbon sources

Definition of D-gluconate catabolism

# In most bacteria, gluconate degradation proceeds via D-gluconate 6-phosphate 
# and either the Entner-Doudoroff pathway or the oxidative pentose phosphate pathway (metacyc:GLUCONSUPER-PWY).
# Alternatively, gluconate can be oxidized in the periplasm to
# 2-ketogluconate before uptake (metacyc:DHGLUCONATE-PYR-CAT-PWY).

# A TRAP type transporter for gluconate is described in Sinorhizobium meliloti (PMID:19060150).
# SMa0249 (gntA, Q930R3) is the small permease component.
# SMa0250 (gntB, Q930R2) is the large permease component.
# SMa0252 (gntC, Q930R1) is the periplasmic solute-binding component.
# Fitness data identified related systems in Azospirillum brasilense Sp245, Pseudomona stutzeri RCH2, Acidovorax sp. GW101-3H11.
#   AZOBR_RS15925 = AZOBR_p130075 = G8AR26 is the small permease component; it was originally
#     annotated as a pseudogene.
#   AZOBR_RS15920 is the large permease component.
#   AZOBR_RS15915 = G8AR24 is the solute receptor (DctP-like) .
# In psRCH2, these are Psest_2123, Psest_2124, Psest_2125 (GFF2080:GFF2082); the small permease component
#     is fused to gluconokinase.
# In Acidovorax, these are Ac3H11_3228 (A0A165IVI0), Ac3H11_3227 (A0A165IWV9), Ac3H11_3226 (A0A165IVH1).
gntA	gluconate TRAP transporter, small permease component	uniprot:Q930R3	uniprot:G8AR26	curated:reanno::psRCH2:GFF2080	uniprot:A0A165IVI0
gntB	gluconate TRAP transporter, large permease component	uniprot:Q930R2	curated:reanno::azobra:AZOBR_RS15920	curated:reanno::psRCH2:GFF2081	uniprot:A0A165IWV9
gntC	gluconate TRAP transporter, periplasmic solute-binding component	uniprot:Q930R1	uniprot:G8AR24	curated:reanno::psRCH2:GFF2082	uniprot:A0A165IVH1

# Transporters and PTS systems were identified using
# query: transporter:gluconate:D-gluconate
gluconate-transport: gntA gntB gntC

# Ignore TC 4.A.6.1.14 / Q8DR76 which transports disaccharides of glucuronate

gntEIIA	gluconate PTS system, IIA component	curated:TCDB::Q82ZC8
gntEIIB	gluconate PTS system, IIB component	curated:TCDB::Q82ZC7
gntEIIC	gluconate PTS system, IIC component	curated:TCDB::Q82ZC5
gntEIID	gluconate PTS system, IID component	curated:TCDB::Q82ZC6
# PTS systems (forming 6-phosphogluconate)
gluconate-PTS: gntEIIA gntEIIB gntEIIC gntEIID

gntT	gluconate:H+ symporter GntT	curated:SwissProt::P39344	curated:SwissProt::P39835	curated:TCDB::P0AC94	curated:TCDB::P0AC96	curated:TCDB::P12012	curated:reanno::BFirm:BPHYT_RS16725	curated:reanno::Cup4G11:RR42_RS28835
gluconate-transport: gntT

ght3	gluconate transporter Ght3	curated:CharProtDB::CH_091200
gluconate-transport: ght3

# Ignore CharProtDB::CH_122791 (PTH1), not actually characterized
# Ignore Gluconate transport inducer 1 (O14367)
# Ignore the non-specific transporter ClC-5

# Psest_2123 (GFF2080) is a fusion of the TRAP component and gluconate kinase (but was not given the EC number)
# CH_125646 is annotated as gluconokinase but was not given the EC number
gntK	D-gluconate kinase	EC:2.7.1.12	curated:reanno::psRCH2:GFF2080	ignore:BRENDA::Q61036	ignore:BRENDA::Q29502	curated:CharProtDB::CH_125646

# Cytoplasmic gluconate 6-phosphate can be formed by PTS systems or by the kinase gntK.
to-gluconate-6-phosphate: gluconate-PTS
to-gluconate-6-phosphate: gluconate-transport gntK

# This forms ribulose-5-phosphate, which is an intermediate in the pentose phosphate pathway
gnd	6-phosphogluconate dehydrogenase, decarboxylating	EC:1.1.1.44	EC:1.1.1.343

import glucose.steps:edd eda gadh1 gadh2 gadh3 kguT kguK kguD

# Gluconate 6-phosphate can be consumed by the Entner-Doudoroff pathway (edd and eda) or by
# oxidative decarboxylation (by gnd) to ribulose 5-phosphate, an intermediate in the pentose phosphate
# pathway. Alternatively, if gluconate is oxidized to 2-ketogluconate in the periplasm (by gadh123), it
# can be taken up by kguT, phosphorylated, reduced to gluconate 6-phosphate, and consumed
# by the Entner-Doudoroff pathway.
all: to-gluconate-6-phosphate edd eda
all: to-gluconate-6-phosphate gnd
all: gadh1 gadh2 gadh3 kguT kguK kguD edd 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:

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