GapMind for catabolism of small carbon sources


D-gluconate catabolism in Burkholderia phytofirmans PsJN

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gadh1 gluconate 2-dehydrogenase flavoprotein subunit BPHYT_RS23025 BPHYT_RS30780
gadh2 gluconate 2-dehydrogenase cytochrome c subunit BPHYT_RS23020 BPHYT_RS01060
gadh3 gluconate 2-dehydrogenase subunit 3 BPHYT_RS23030 BPHYT_RS01070
kguT 2-ketogluconate transporter BPHYT_RS11295 BPHYT_RS10985
kguK 2-ketogluconokinase BPHYT_RS11300
kguD 2-keto-6-phosphogluconate reductase BPHYT_RS11290 BPHYT_RS14520
edd phosphogluconate dehydratase BPHYT_RS16735 BPHYT_RS04815
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BPHYT_RS16730 BPHYT_RS16945
Alternative steps:
ght3 gluconate transporter Ght3
gnd 6-phosphogluconate dehydrogenase, decarboxylating BPHYT_RS29625 BPHYT_RS26220
gntA gluconate TRAP transporter, small permease component
gntB gluconate TRAP transporter, large permease component BPHYT_RS30450 BPHYT_RS24185
gntC gluconate TRAP transporter, periplasmic solute-binding component BPHYT_RS35760 BPHYT_RS24175
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 BPHYT_RS16720
gntT gluconate:H+ symporter GntT BPHYT_RS16725 BPHYT_RS13375

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.



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:

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