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GO-CAM purine metabolism/ adenine biosynthesis #3699

Open ValWood opened 2 months ago

ValWood commented 2 months ago

https://en.wikipedia.org/wiki/Purine_metabolism#:~:text=Purines%20are%20biologically%20synthesized%20as,completely%20formed%20purine%20ring%20system.

ValWood commented 2 months ago
nucleotide biosynthesis
ValWood commented 2 months ago

A nice straightforward one. This wasn't on the priority list but I opened this ticket when Henry asked about it last week. I guess it is a nice one to do

PCarme commented 1 month ago

I did this one. You can have a look on Noctua, see if you notice anything wrong or missing.

ValWood commented 1 month ago

This looks great to me. Some of the processes look a bit weird, but this is an issue with GO, and the existing annotation rather than your model (i.e, when we have terms for the biosynthesis or catabolism of intermediates). The model structure looks correct.

could you check if these fit into the model:

SPBC106.04 ada1 adenosine deaminase Ada1
SPCC338.14 ado1 adenosine kinase
SPAP7G5.02c gua2 GMP synthase [glutamine-hydrolyzing] Gua2
SPBC1198.05 guk1 guanylate kinase Guk1
SPAC806.07 ndk1 nucleoside diphosphate kinase Ndk1

SPBC106.04 ada1 adenosine deaminase Ada1 SPCC338.14 ado1 adenosine kinase SPAP7G5.02c gua2 GMP synthase [glutamine-hydrolyzing] Gua2 SPBC1198.05 guk1 guanylate kinase Guk1 SPAC806.07 ndk1 nucleoside diphosphate kinase Ndk1

PCarme commented 1 month ago

Gua2 and Guk1 are already in the model, and I just added Ada1. I guess I will have to add the ATP and GTP synthesis before I can fit Ado1 and Ndk1 into the model.

ValWood commented 1 month ago

It is possible that the existing annotations on these could be wrong.

If you spot any incorrect inferences that are IBA or IEA evidence you can report them here: https://github.com/geneontology/go-annotation/issues

any ISS,ISO,IC,NAS,TAS are usually ours. You can report these on the PomBase curation tracker and I will remove them.

Legacy experimental could be ours, or UniProt, report those on out tracker and I will review. Once you are set up with svn I'll show you where to edit these.