FEV_KEGG.Experiments.14 module

Question

Which percentage of EC numbers is shared between all organisms of Escherichia coli K-12?

Method

  • Get all metabolic pathways of all E. coli organisms from KEGG.
  • For each organisms, combine all pathways to the metabolic network, by UNION operation.
  • Convert this metabolic network into a substance-ecNumber graph.
  • Combine all organisms’ networks to a single unified E. coli network, by UNION operation.
  • Combine all organisms’ networks to a consensus network, by INTERSECT operation, leaving only substances and EC numbers that occur in all organisms.
  • Print number of EC numbers in the unified network -> numberUnified.
  • Print number of EC numbers in the consensus network -> numberConsensus.
  • Print percentage numberConsensus/numberUnified.

Result

unified: 617
consensus: 560
90.76175040518638%

Conclusion

About 91% of all EC numbers present in all known Escherichia coli K-12 organisms occur in all organisms. Thus, 9% of EC numbers only occur in some of the organisms. This indicates that organisms evolve by acquiring new enzymatic functionalities. Whether they stem from neofunctionalisation, horizontal gene transfer, or genesis remains to be investigated.