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C-CoMP-STC / GEM-mit1002

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Run MEMOTE on new model before gap filling #33

Closed hgscott closed 11 months ago

hgscott commented 11 months ago

See what biomass reactions are blocked.

Could also use our own custom tool for checking for blocked biomass components.

hgscott commented 11 months ago

GitHub actions did this the second I pushed the new file, thanks past Helen!

The file is here: https://github.com/C-CoMP-STC/GEM-mit1002/blob/ms2_model/index.html

and it looks like this: Image

Big take away- 22 biomass components are blocked: Image

hgscott commented 11 months ago

I wrote a little function to take the biomass component list and print out a table in markdown format:

def print_component_table(model, blocked_components):
    print("| ID | Name |")
    print("| --- | --- |")
    for component in blocked_components:
        print("| " + component + " | " + model.metabolites.get_by_id(component).name + " |")
The blocked biomass components are: ID Name
cpd00220_c0 Riboflavin [c0]
cpd00201_c0 10-Formyltetrahydrofolate [c0]
cpd15352_c0 2-Demethylmenaquinone 8 [c0]
cpd00056_c0 TPP [c0]
cpd00345_c0 5-Methyltetrahydrofolate [c0]
cpd00010_c0 CoA [c0]
cpd00118_c0 Putrescine [c0]
cpd00254_c0 Mg [c0]
cpd00099_c0 Cl- [c0]
cpd15500_c0 Menaquinone 8 [c0]
cpd00149_c0 Co2+ [c0]
cpd15793_c0 Stearoylcardiolipin (B. subtilis) [c0]
cpd00557_c0 Siroheme [c0]
cpd11493_c0 ACP [c0]
cpd10515_c0 Fe2+ [c0]
cpd00087_c0 Tetrahydrofolate [c0]
cpd11463_c0 Protein [c0]
cpd02229_c0 Bactoprenyl diphosphate [c0]
cpd15665_c0 Peptidoglycan polymer (n subunits) [c0]
cpd00264_c0 Spermidine [c0]
cpd15560_c0 Ubiquinone-8 [c0]
cpd00015_c0 FAD [c0]
hgscott commented 11 months ago

Some of these just look like we need a transporter, ie. Co2+. The vitamins we may want to add a transporter, but the bacteria may also be able to make those? The fact that all protein is blocked makes me think there is something big missing.