D-gluconate catabolism in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

D-gluconate catabolism in Dinoroseobacter shibae DFL-12

Best path

Also see fitness data for the top candidates

Rules

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

all:

to-gluconate-6-phosphate, edd and eda
or to-gluconate-6-phosphate and gnd
or gadh1, gadh2, gadh3, kguT, kguK, kguD, edd and eda
Comment: 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.

to-gluconate-6-phosphate:

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

gluconate-PTS: gntEIIA, gntEIIB, gntEIIC and gntEIID

Comment: PTS systems (forming 6-phosphogluconate)

gluconate-transport:

gntA, gntB and gntC
or gntT
or ght3
Comment: Transporters and PTS systems were identified using query: transporter:gluconate:D-gluconate

19 steps (8 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
gntT	gluconate:H+ symporter GntT
gntK	D-gluconate kinase
edd	phosphogluconate dehydratase	Dshi_1769	Dshi_0129
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	Dshi_1768	Dshi_1241
Alternative steps:
gadh1	gluconate 2-dehydrogenase flavoprotein subunit	Dshi_3895
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	Dshi_4060	Dshi_3784
gadh3	gluconate 2-dehydrogenase subunit 3	Dshi_3896
ght3	gluconate transporter Ght3
gnd	6-phosphogluconate dehydrogenase, decarboxylating
gntA	gluconate TRAP transporter, small permease component
gntB	gluconate TRAP transporter, large permease component	Dshi_2753	Dshi_3709
gntC	gluconate TRAP transporter, periplasmic solute-binding component	Dshi_3326	Dshi_0958
gntEIIA	gluconate PTS system, IIA component
gntEIIB	gluconate PTS system, IIB component
gntEIIC	gluconate PTS system, IIC component
gntEIID	gluconate PTS system, IID component
kguD	2-keto-6-phosphogluconate reductase	Dshi_2970	Dshi_2643
kguK	2-ketogluconokinase
kguT	2-ketogluconate transporter

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.

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