GapMind for catabolism of small carbon sources


D-gluconate catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda

Also see fitness data for the top candidates


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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gadh1 gluconate 2-dehydrogenase flavoprotein subunit AO353_10795
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AO353_10800 AO353_27065
gadh3 gluconate 2-dehydrogenase subunit 3 AO353_10790
kguT 2-ketogluconate transporter AO353_26880 AO353_26910
kguK 2-ketogluconokinase AO353_26875
kguD 2-keto-6-phosphogluconate reductase AO353_04850 AO353_26885
edd phosphogluconate dehydratase AO353_03420 AO353_08345
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO353_03350 AO353_01265
Alternative steps:
ght3 gluconate transporter Ght3
gnd 6-phosphogluconate dehydrogenase, decarboxylating AO353_25835
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
gntEIIB gluconate PTS system, IIB component
gntEIIC gluconate PTS system, IIC component
gntEIID gluconate PTS system, IID component
gntK D-gluconate kinase AO353_03250
gntT gluconate:H+ symporter GntT AO353_05900 AO353_03245

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:

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