Analysis of metabolic and other functional capabilities#
I wrote a Python script to extract ID, genes and their functions from the annotations files, and classified the genes into several functional categories as in the paper. As expected, genes in different metabolic systems were identified.
Energy conservation: ATP synthase, NADH dehydrogenase, etc.
Carbon fixation: reductive TCA cycle
Nitrogen fixation: nitrogenase complex
Metal resistance: As/Cu/Ag/Cd/Co/Zn/Hg efflux pump
Chemotaxis and motility: movement in response to a chemical stimulus, assembly of flagella, sensing environmental signals
Oxidative stress response: reactive oxygen species (ROS) degradation, production of antioxidants
Biofilm formation: cellulose production, polysaccharide synthesis and export
Results are written in these two tables for investigation as well as deeper analysis.