Ability to distingush "unknown" steps from "constitutively upstream"

[ValWood]

If I have pathways with a gap, and here it would be really nice to be able to put a big red "?" instead of "constitutively upstream" (sometimes we might use constitutively upstream for committed chunks of processes like transcription), or in the case of the arginine biosynthesis pathway we know the entire metabolic pathway, but there is an unknown citrulline carrier between arg3 and arg12 so the pathway looks complete but it isn't:

I would like to annotate as arg3 -> ? -> arg12 so that gaps in pathways can easily be identified for computational purposes (and for the projects studying unknown proteins).

CC @PCarme

[thomaspd]

You should be able to add an activity that has no gene product associated with it (i.e. just use "information biomacromolecule" in the enabled_by field), and connect it into your model.

[ValWood]

Thanks we will try this!
@ CC @PCarme

[ValWood]

It would be cool if this displayed as a [? unknown] (information biomolecule is a bit cryptic)

[pgaudet]

I think you can use ChEBI:protein (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=36080), which is a bit less cryptic