GapMind for catabolism of small carbon sources

 

Definition of D-glucose catabolism

As rules and steps, or see full text

Rules

Overview: In most bacteria, glucose is consumed via glucose 6-phosphate, which is a central metabolic intermediate. It can also be oxidized to 2-ketogluconate in the periplasm before uptake and conversion to gluconate 6-phosphate (link). Periplasmic oxidation to gluconate, uptake, and phosphorylation by gnuK is also a potential path to gluconate-6-phosphate, but is not included in GapMind because it is not known to be the major path for glucose utilization in a prokaryote.

Steps

MFS-glucose: glucose transporter, MFS superfamily

SSS-glucose: Sodium/glucose cotransporter

glcU': Glucose uptake protein GlcU

PAST-A: proton-associated sugar transporter A

SemiSWEET: Sugar transporter SemiSWEET

SWEET1: bidirectional sugar transporter SWEET1

mglA: glucose ABC transporter, ATP-binding component (MglA)

mglB: glucose ABC transporter, substrate-binding component

mglC: glucose ABC transporter, permease component (MglC)

gtsA: glucose ABC transporter, substrate-binding component (GtsA)

gtsB: glucose ABC transporter, permease component 1 (GtsB)

gtsC: glucose ABC transporter, permease component 2 (GtsC)

gtsD: glucose ABC transporter, ATPase component (GtsD)

glcS: glucose ABC transporter, substrate-binding component (GlcS)

glcT: glucose ABC transporter, permease component 1 (GlcT)

glcU: glucose ABC transporter, permease component 2 (GlcU)

glcV: glucose ABC transporter, ATPase component (GclV)

aglE': glucose ABC transporter, substrate-binding component (AglE)

aglF': glucose ABC transporter, permease component 1 (AglF)

aglG': glucose ABC transporter, permease component 2 (AglG)

aglK': glucose ABC transporter, ATPase component (AglK)

ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)

bglF: glucose PTS, enzyme II (BCA components, BglF)

ptsG: glucose PTS, enzyme IICB

crr: glucose PTS, enzyme IIA

manX: glucose PTS, enzyme EIIAB

manY: glucose PTS, enzyme EIIC

manZ: glucose PTS, enzyme EIID

glk: glucokinase

gdh: quinoprotein glucose dehydrogenase

gnl: gluconolactonase

gadh1: gluconate 2-dehydrogenase flavoprotein subunit

gadh2: gluconate 2-dehydrogenase cytochrome c subunit

gadh3: gluconate 2-dehydrogenase subunit 3

kguT: 2-ketogluconate transporter

kguK: 2-ketogluconokinase

kguD: 2-keto-6-phosphogluconate reductase

edd: phosphogluconate dehydratase

eda: 2-keto-3-deoxygluconate 6-phosphate aldolase

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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