FEV_KEGG.Experiments.54 module

Context

Combining the list of all neofunctionalisations, sorted by their function change, from 51, and the list of neofunctionalisations contributing to robustness, sorted by the EC number they provide robustness for, from 53.

E-value also plays an important role in the number of neofunctionalisations reported, because the bigger the E-value is, the easier two enzymes match as gene-duplicates, the higher the probability of a discovered function change, together resulting in a neofunctionalisation.

Question

Which neofunctionalisations exist in the core metabolism of Archaea, using a certain E-value? Grouped by function change, sorted lexicographically, annotated with links to KEGG, annotated with human-readable names (if possible), and exported into an HTML file.

Which neofunctionalised enzymes cause the core metabolism of Archaea to have increased redundancy? Grouped by contributed functions, sorted lexicographically, annotated with links to KEGG, annotated with human-readable names (if possible), and exported into an HTML file.

Method

  • get clade
  • get core metabolism
  • calculate “neofunctionalised” ECs
  • report neofunctionalisations
  • print them into nice HTML
  • calculate redundancy
  • REPEAT for each “neofunctionalised” EC contributing to redundancy
  • report enzyme pairs of neofunctionalisations, which caused the EC to be considered “neofunctionalised”, and are in return contributing to redundancy
  • print them into nice HTML

Result

core metabolism majority: 80%
neofunctionalisation majority: 0% (this means that gene duplication within a single organism is enough)

Archaea:

core metabolism ECs: 114


All neofunctionalisations: 1140
    [see Archaea_Neofunctionalisations-For-FunctionChange.html]

"neofunctionalised" ECs: 16 (14%)

Neofunctionalisations contributing to robustness: 93 (8%)
    [see Archaea_Neofunctionalisations-For-Contributed-EC.html]

Conclusion

Archaea do not seem to have many neofunctionalisations contributing to robustness. This might be limited by: - the size of the core metabolism, i.e. the majority percentage. - the E-value. The lower the E-value, the closer two enzymes’ sequences have to match, for them to be recognised as gene-duplicated. Using a higher E-value will greatly increase the number of neofunctionalisations reported. Of course, this will also increase the number of false-positives.

FEV_KEGG.Experiments.54.getClade()[source]