FEV_KEGG.Experiments.52 module¶
Context¶
In 49, we did this before, but this time we export into pretty HTML.
Question¶
Which neofunctionalised enzymes cause the core metabolism of Deltaproteobacteria to have increased redundancy? How much do they contribute? 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
- 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)
Deltaproteobacteria:
core metabolism ECs: 228
"neofunctionalised" ECs: 36 (16%)
Neofunctionalisations contributing to robustness: 84
[see file Deltaproteobacteria_ROBUSTNESS_Neofunctionalisations-For-Contributed-EC.html]
Conclusion¶
Much more useful than a plain text list of cryptic IDs.
The well-known neofunctionalisation 2.6.1.1 <-> 2.6.1.9 does not occur here. Maybe the core metabolism’s majority percentage is too high, or both of the two EC numbers can only contribute to partial redundancy?