D-gluconate catabolism in Hafnia paralvei ATCC 29927

GapMind for catabolism of small carbon sources

D-gluconate catabolism in Hafnia paralvei ATCC 29927

Best path

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 (14 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
gntT	gluconate:H+ symporter GntT	M988_RS19705	M988_RS07980
gntK	D-gluconate kinase	M988_RS19700	M988_RS07975
edd	phosphogluconate dehydratase	M988_RS10980	M988_RS01845
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	M988_RS13025	M988_RS10975
Alternative steps:
gadh1	gluconate 2-dehydrogenase flavoprotein subunit	M988_RS12890	M988_RS10760
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	M988_RS12885	M988_RS10765
gadh3	gluconate 2-dehydrogenase subunit 3	M988_RS12895	M988_RS10755
ght3	gluconate transporter Ght3
gnd	6-phosphogluconate dehydrogenase, decarboxylating	M988_RS07450
gntA	gluconate TRAP transporter, small permease component
gntB	gluconate TRAP transporter, large permease component
gntC	gluconate TRAP transporter, periplasmic solute-binding component
gntEIIA	gluconate PTS system, IIA component	M988_RS15850
gntEIIB	gluconate PTS system, IIB component
gntEIIC	gluconate PTS system, IIC component	M988_RS13040
gntEIID	gluconate PTS system, IID component	M988_RS13035	M988_RS08920
kguD	2-keto-6-phosphogluconate reductase	M988_RS00465	M988_RS00055
kguK	2-ketogluconokinase	M988_RS00065
kguT	2-ketogluconate transporter	M988_RS00060	M988_RS02580

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