FEV_KEGG.Experiments.55 module¶
Context¶
Extending 54 by a list of all the alternative paths each neofunctionalisation (or rather one of their EC numbers) occurs on.
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. Also listing each alternative path a neofunctionalisation occurs on, contributing to redundancy of the current group’s redundant EC number.
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
- report the alternative paths constituting the 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]