FEV_KEGG.Experiments.44 module¶
Question¶
Which EC numbers are linked with neofunctionalisations in Deltaproteobacteria and Spirochaetes? How do the two groups compare?
Method¶
- get both clades
- calculate set of “neofunctionalised” ECs for Alphaproteobacteria
- calculate set of “neofunctionalised” ECs for Betaproteobacteria
- REPEAT for varying core metabolism majority-percentages:
- overlap sets and print amount of EC numbers inside the intersection and falling off either side
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%)
1.1.1.42
1.1.1.85
2.1.3.2
2.1.3.3
2.2.1.1
2.2.1.7
2.4.2.14
2.5.1.47
2.6.1.1
2.6.1.16
2.6.1.62
2.6.1.9
4.1.3.-
4.2.1.46
5.1.1.1
5.1.3.2
5.1.3.6
5.3.1.16
5.4.3.8
5.4.99.18
6.1.1.12
6.1.1.16
6.1.1.17
6.1.1.18
6.1.1.22
6.1.1.4
6.1.1.5
6.1.1.6
6.1.1.9
6.2.1.1
6.2.1.3
6.3.2.10
6.3.2.13
6.3.2.8
6.3.2.9
6.3.4.13
Spirochaetes:
core metabolism ECs: 80
"neofunctionalised" ECs: 10 (12%)
6.1.1.10
6.1.1.12
6.1.1.20
6.1.1.22
6.1.1.4
6.1.1.5
6.1.1.6
6.1.1.9
6.3.2.13
6.3.2.8
Comparison:
100%: 0 2 3
80%: 28 8 2
60%: 47 8 4
40%: 72 20 8
20%: 125 40 14
Conclusion¶
Deltaproteobacteria consistently have more “neofunctionalised” EC numbers, which is not surprising, as the core metabolism is much bigger. The same effect explains the constant increase in “neofunctionalised” EC numbers with growing core metabolism, due to lower majority-percentage. This indicates that neofunctionalisation is widespread and not limited to the most important, hence widespread, parts of metabolism. However, there might still be a statistical skew which remains to be investigated.
Occurence in these results above does not mean, that those ECs are actually “neofunctionalised” in all of the organisms! Because in this experiment, a single neofunctionalisation is enough to mark the associated ECs as “neofunctionalised”. It might be interesting to increase the neofunctionalisation majority percentage, to only include ECs which have neofunctionalisations in x% of the clade’s organisms.