Hi,
Firstly, thanks for this tool - it’s super useful.
I’m a little confused about the way pathways are determined.
I noticed that the pathway Pathway: L-ascorbate biosynthesis IV (animals, D-glucuronate pathway) is being identified in a number of my samples - which I thought was a bit weird - but I thought this may be due to gap filling (which only allows for one missing reaction right?)
But on closer inspection of the reactions (using humann_regroup_table) and this file - more than one non-spontaneous reaction is missing from this pathway in all samples (RXN3DJ-64, GLUCURONATE-REDUCTASE, L-GULONOLACTONE-OXIDASE).
However, I then realised it was more complicated than that with some reactions being optional? (how is this determined?)
For example, for this pathway:
PWY3DJ-35471 PHOSPHOGLUCMUT-RXN GLUC1PURIDYLTRANS-RXN UGD-RXN -RXN3DJ-64 ( -RXN-14693 , GLUCURONATE-REDUCTASE-RXN ) RXN-8783 -L-GULONOLACTONE-OXIDASE-RXN -RXN-878
So does this mean that only PHOSPHOGLUCMUT-RXN GLUC1PURIDYLTRANS-RXN UGD-RXN and RXN-8783 are required?
If so, why does turning gap-filling off then make this pathway disappear, despite a number of samples with all four of these reactions?
Cheers and thanks in advance!