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This repository hosts the tracker for issues pertaining to GO annotations.
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Incorrect Unirule mapping: GO:0070814 | hydrogen sulfide biosynthetic process | IEA with UPA00140 #5401

Open ValWood opened 3 months ago

ValWood commented 3 months ago

UniProt UniRule (ID and label):

Sequences with problematic annotation (ID + gene/protein name):

https://www.pombase.org/gene/SPAC1782.11

Description of issue

GO:0070814 | hydrogen sulfide biosynthetic process | IEA with UPA00140 | GO_REF:0000041

This is part of sulphate assimilation, maybe the hydrogen sulfide biosynthetic process is something bacterial?

ValWood commented 3 months ago

Also https://www.pombase.org/gene/SPBC27.08c

ValWood commented 3 months ago

I think this is the case:

The Sulfate Reducing Pathway: This pathway is more common in sulfate-reducing bacteria and archaea. It involves the reduction of sulfate to hydrogen sulfide (H₂S), which is then used for various metabolic processes.

in yeast its The Adenosine Phosphosulfate (APS) Pathway: This is the primary sulfate assimilation pathway in plants, bacteria, and some fungi. It involves the reduction of sulfate (SO₄²⁻) to sulfide (S²⁻) through a series of intermediates, including adenosine 5'-phosphosulfate (APS) and 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The sulfide is then incorporated into cysteine and other sulfur-containing compounds.

but they probably have shared enzymes?

ValWood commented 3 months ago

Actually hydrogen sulphide is the output, ignore

ValWood commented 3 months ago

I did a bit more digging here because there were multiple ways to describe the same pathway

sufate assimilation vs hydrogen sulphide biosynthesis.

It seems that although hydrogen sulphide can be formed via these pathways it is usually incorporated into amino acids like cysteine rather than being released as H₂S. Therefore, this pathway is more about biosynthesis of sulfur-containing compounds rather than H₂S specifically. They are not primarily considered hydrogen sulfide biosynthesis pathways. The term "hydrogen sulfide biosynthesis" is more accurately applied to processes like dissimilatory sulfate reduction carried out by sulfate-reducing bacteria, where the production of H₂S is the primary outcome. SO I will filer this term and ask for a taxon restriction after all.