GapMind for catabolism of small carbon sources

 

D-gluconate catabolism in Thioclava dalianensis DLFJ1-1

Best path

gntA, gntB, gntC, gntK, edd, eda

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gntA gluconate TRAP transporter, small permease component DL1_RS12260 DL1_RS16600
gntB gluconate TRAP transporter, large permease component DL1_RS12255 DL1_RS12440
gntC gluconate TRAP transporter, periplasmic solute-binding component DL1_RS12250 DL1_RS12450
gntK D-gluconate kinase DL1_RS06040
edd phosphogluconate dehydratase DL1_RS12880 DL1_RS11965
eda 2-keto-3-deoxygluconate 6-phosphate aldolase DL1_RS12885 DL1_RS05975
Alternative steps:
gadh1 gluconate 2-dehydrogenase flavoprotein subunit DL1_RS19555
gadh2 gluconate 2-dehydrogenase cytochrome c subunit DL1_RS19560 DL1_RS20615
gadh3 gluconate 2-dehydrogenase subunit 3 DL1_RS19550
ght3 gluconate transporter Ght3
gnd 6-phosphogluconate dehydrogenase, decarboxylating DL1_RS14430
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 DL1_RS07935 DL1_RS07735
kguK 2-ketogluconokinase DL1_RS12510
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.

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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