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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 1 year ago

hgscott commented 1 year ago

See what biomass reactions are blocked.

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

hgscott commented 1 year 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 1 year 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 1 year 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.