import/export and exchange rxn missing for dihydroorotate

[johan-gson]

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Description of the issue:

The metabolite (S)-dihydroorotate[c] is reported to be exported by cells (see https://www.nature.com/articles/s41467-018-08033-9 ), but there is no export rxn (and I assume there should be an import rxn as well). There is no exch rxn either. I have no idea about GPR though. This is happening in hypoxia.

Expected feature/value/output:

Just add the reactions I'm thinking, i.e. (S)-dihydroorotate[c] <=> (S)-dihydroorotate[s] (S)-dihydroorotate[s] <=>

Current feature/value/output:

Reproducing these results:

I hereby confirm that I have:

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

[JonathanRob]

Thanks for spotting this. Though I guess now we would abbreviate the compartment as [e] rather than [s].

[mihai-sysbio]

Looking a bit more into this, the annotation for these reactions doesn't look straightforward.

A name search for (S)-dihydroorotate returned CHEBI:30864, but that is different from CHEBI:17025 which is the annotation of MAM00180c. In fact, the CHEBI name for MAM00180c is (S)-dihydroorotic acid.

Overlooking the potentially misannotated metabolite, some transport reactions for (S)-dihydroorotate seem to exist in MNX.

[johan-gson]

Yeah, it is with this for many compounds, that you can either talk about the ion or the acid (which includes the H+). It is the same with for example the amino acid glutamate/glutamic acid