gntA, gntB, gntC, gntK, edd, eda
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).
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
gntA | gluconate TRAP transporter, small permease component | CRO07_RS06720 | |
gntB | gluconate TRAP transporter, large permease component | CRO07_RS06715 | |
gntC | gluconate TRAP transporter, periplasmic solute-binding component | CRO07_RS06725 | CRO07_RS11160 |
gntK | D-gluconate kinase | ||
edd | phosphogluconate dehydratase | CRO07_RS01200 | CRO07_RS16225 |
eda | 2-keto-3-deoxygluconate 6-phosphate aldolase | CRO07_RS01195 | |
Alternative steps: | |||
gadh1 | gluconate 2-dehydrogenase flavoprotein subunit | ||
gadh2 | gluconate 2-dehydrogenase cytochrome c subunit | CRO07_RS10535 | |
gadh3 | gluconate 2-dehydrogenase subunit 3 | ||
ght3 | gluconate transporter Ght3 | ||
gnd | 6-phosphogluconate dehydrogenase, decarboxylating | ||
gntEIIA | gluconate PTS system, IIA component | ||
gntEIIB | gluconate PTS system, IIB component | ||
gntEIIC | gluconate PTS system, IIC component | ||
gntEIID | gluconate PTS system, IID component | ||
gntT | gluconate:H+ symporter GntT | ||
kguD | 2-keto-6-phosphogluconate reductase | CRO07_RS11825 | CRO07_RS10960 |
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 24 2021. The underlying query database was built on Sep 17 2021.
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:
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