FEV_KEGG.Experiments.48 module¶
Question¶
Which “neofunctionalised” EC numbers exist in Deltaproteobacteria? Does their existence increase redundancy? If yes, how much?
Method¶
- get Deltaproteobacteria
- get “neofunctionalised” ECs
- calculate redundancy
- REPEAT for each “neofunctionalised” EC
- print number of ECs the “neofunctionalised” EC provides redundancy for (robustness and flexibility)
- print ECs which have “neofunctionalised” ECs contributing to their robustness
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 (0 target-flexibility) (0 robustness) 1.1.1.85 (0 target-flexibility) (0 robustness) 2.1.3.2 (0 target-flexibility) (0 robustness) 2.1.3.3 (1 target-flexibility) (0 robustness) 2.2.1.1 (6 target-flexibility) (2 robustness) 2.2.1.7 (7 target-flexibility) (2 robustness) 2.4.2.14 (2 target-flexibility) (0 robustness) 2.5.1.47 (0 target-flexibility) (0 robustness) 2.6.1.1 (2 target-flexibility) (0 robustness) 2.6.1.16 (2 target-flexibility) (0 robustness) 2.6.1.62 (0 target-flexibility) (0 robustness) 2.6.1.9 (0 target-flexibility) (0 robustness) 4.1.3.- (1 target-flexibility) (1 robustness) 4.2.1.46 (0 target-flexibility) (0 robustness) 5.1.1.1 (1 target-flexibility) (0 robustness) 5.1.3.2 (2 target-flexibility) (0 robustness) 5.1.3.6 (1 target-flexibility) (0 robustness) 5.3.1.16 (0 target-flexibility) (0 robustness) 5.4.3.8 (0 target-flexibility) (0 robustness) 5.4.99.18 (1 target-flexibility) (0 robustness) 6.1.1.12 (1 target-flexibility) (0 robustness) 6.1.1.16 (0 target-flexibility) (0 robustness) 6.1.1.17 (0 target-flexibility) (0 robustness) 6.1.1.18 (1 target-flexibility) (0 robustness) 6.1.1.22 (0 target-flexibility) (0 robustness) 6.1.1.4 (0 target-flexibility) (0 robustness) 6.1.1.5 (0 target-flexibility) (0 robustness) 6.1.1.6 (0 target-flexibility) (0 robustness) 6.1.1.9 (0 target-flexibility) (0 robustness) 6.2.1.1 (3 target-flexibility) (0 robustness) 6.2.1.3 (0 target-flexibility) (0 robustness) 6.3.2.10 (0 target-flexibility) (0 robustness) 6.3.2.13 (0 target-flexibility) (0 robustness) 6.3.2.8 (0 target-flexibility) (0 robustness) 6.3.2.9 (0 target-flexibility) (0 robustness) 6.3.4.13 (0 target-flexibility) (0 robustness)
Target-flexibility: 17.1% Target-flexibility contribution: 46.2%
Robustness: 7.0% Robustness contribution: 31.2%
Robust ECs contributed by “neofunctionalised” ECs: [1.2.1.12, 2.2.1.2, 2.4.2.-, 2.7.9.2, 5.1.3.1]
Conclusion¶
31.2% of the core metabolism’s robust EC numbers have at least one redundant path, making this EC number robust, which contains a “neofunctionalised” EC number. 7% of the core metabolism’s EC numbers are robust. This makes a total of 7% * 31.2% = 2.18% * 228 ECs in the core metabolism = 5 EC numbers in the core metabolism, which are robust with a “neofunctionalised” EC number on at least one of their alternative paths.