The bigg_e_coli_core Escherichia coli K12
model is a simplified metabolic network model and is (almost) identical to the model published as supporting
material in Orth
et al. (2010). The following exercises are inspired by this document.
Warming up
Initialization:
- Reset your session
- Pick the bigg_e_coli_core E. coli model from the model and pathway repository
To get familiar with the website's interface, please answer the following questions about the bigg_e_coli_core model:
- What is the total number of reactions?
- What is the total number of external (boundary) reactions?
Please distinguish between uptake and secretion reactions.
- What are the total numbers of reversible/irreversible reactions?
- Can you identify any reactions with a fixed reaction flux? If so, what
does this mean?
- What is the total number of metabolites?
- What are the dimensions of the stoichiometric matrix for the
considered model?
- What compartments are considered in the model? Are there any
compartments missing?
- What additional compartments could be relevant for an
eukaryotic model?
- How many metabolites does the biomass reaction comprise? What
does the biomass reaction represent? Are there potential extensions?
- How many reactions are connected to the biomass reaction?
- How many reactions occur in a single
compartment only? What kind of reactions are the remaining
reactions? What is their total number?
- How many reactions are orphans, i.e. reactions without protein
association? Which reaction comprises the most proteins or protein complexes?
- Which protein imports malate into the cytoplasm? How is this
import realized? Can you identify a homolog/homologs in Bacillus subtilis (e.g. use MyHits)?
- What is the shortest path, i.e. number of reactions, between the
external malate and the cytosolic phosphoenolpyruvate?
- In which enzymatic complexes and reactions does the protein PT1_ECOLI
participate?
- In how many different subcellular locations and reactions does
succinate(2-) occur? Can you identify its CHEBI and KEGG ID?
Model boundary
In the reac_list view,
restrict the display to "external" reactions only
by typing BOUNDARY in the Search field. Hint: consider the flux bounds in the Enzy column.
- What can you tell about the growth conditions/environment of
E. coli K12 as modelled by bigg_e_coli_core? What does it mean that some
external reactions are unconstrained/unidirectional/bidirectional?
Simplification
The model bigg_e_coli_core is an oversimplified metabolic network of Escherichia coli strain K12.
- What can you tell about the biomass reaction of this model? Is it biologically relevant?
- What can you tell about the biosynthesis of CoA, ADP, NAD+ and NADP+?
- What can you tell about the sulfur metabolism?
Analyses
Run CR and FBA analyses on the website.
- Does the model grow?
- Can you identify any reaction correlation groups? How do they relate to the flux distribution?
- Can you identify any reaction incoherent correlation groups? Could you explain what's happening with them?
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