Suspected duplicates in the galactose pathway

[johan-gson]

Description of the issue:

There are two metabolites in the model called galactose-1-phosphate[c] alpha-D-galactose-1-phosphate[c]

According to https://pubchem.ncbi.nlm.nih.gov/compound/alpha-D-Galactose-1-phosphate, these are synonyms These are then duplicates (interestingly, they have slightly different GPRs, but the same MNX id (I'm not sure how these work exactly though) ) MAR04130 ATP[c] + galactose[c] => ADP[c] + alpha-D-galactose-1-phosphate[c] + H+[c] MAR04414 ATP[c] + galactose[c] => ADP[c] + galactose-1-phosphate[c] + H+[c]

Also these, although one of them is unidirectional, unclear which it should be. They have the same GPR and same kegg id: MAR04131 glucose-1-phosphate[c] + UDP-galactose[c] <=> alpha-D-galactose-1-phosphate[c] + UDP-glucose[c] MAR04132 galactose-1-phosphate[c] + UDP-glucose[c] => glucose-1-phosphate[c] + UDP-galactose[c] kegg.reaction/R00955

This is the fifth reaction that is concerned (no duplicate found): MAR08767 alpha-D-galactose-1-phosphate[c] + H+[c] + UTP[c] => PPi[c] + UDP-galactose[c]

Galactose metabolism in kegg: https://www.genome.jp/pathway/rn00052+R00955

Expected feature/value/output:

Not sure which to remove, what to do with the GPR (I assume keep the largest one), or what to do with the one that is rev/irrev

Current feature/value/output:

Reproducing these results:

I hereby confirm that I have:

• [X] Tested my code on my own computer for running the model
• [X] Done this analysis in the main branch of the repository
• [X] Checked that a similar issue does not exist already

[haowang-bioinfo]

@johan-gson do you have plan to fix this?

[johan-gson]

Not in the near future, I'm not sure exactly what to do and just got a heavy revision :)