GapMind for catabolism of small carbon sources

 

D-gluconate catabolism in Dinoroseobacter shibae DFL-12

Best path

gntT, gntK, edd, eda

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).

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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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