Plan for designing Azo to depend on Rhodo for carbon

[Jeremy Zucker]

• 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

[James Pino]

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_hom__L_e
EX_tre_e
EX_lyx__L_e
EX_val__L_e
EX_arab__L_e
EX_man_e
EX_leu__L_e
EX_dha_e
EX_glu__L_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?