Plan for designing Azo to depend on Rhodo for carbon

[djinnome]

• Outer loop: for each nutrient:
  • check that axenic rhodo can grow on it, if not break
  • check that axenic azo cannot grow on it, if not break
  • Inner loop: check azo grows in a consortia with rhodo, if not break
    • if it does, find the metabolite that rhodo secretes and azo consumes:
    • collect the metabolite(s) that azo consumes
    • knock out the transporter(s) in rhodo for the secreted metabolite(s)
      • return list of consumed metabolites
      • check that each metabolite is observed to be consumed in azo Biolog
      • check that each metabolite is observed to be secreted in rhodo external metabolites experiment
      • Rank order the list of metabolites by support from experimental evidence

[JamesPino]

Have the results for this in https://github.com/PNNL-CompBio/ConsortiumModels/blob/ternary_growth_on_gly/Notebooks/rt_av_find_biolog_compatible_growth.ipynb

EX_galt_e EX_4abut_e EX_homL_e EX_tre_e EX_lyxL_e EX_valL_e EX_arabL_e EX_man_e EX_leuL_e EX_dha_e EX_gluL_e

where all of these make EX_glyclt_e, which AV can use.

It requires large exchange rates for RT with these compounds, which might not be realistic?