Lysosomal Oligosaccharide catabolism R-HSA-6799545

[ukemi]

• [x] create a mouse model https://github.com/geneontology/pathways2GO/issues/172#issuecomment-1143943080
• [ ] can we make the specificity of the alpha-mannosidases more specific in this model? Looking at the structures in Reactome/ChEBI, I think we can. https://github.com/geneontology/pathways2GO/issues/172#issuecomment-1145077609 [GO:0004569 glycoprotein endo-alpha-1,2-mannosidase activity] [GO:0033915 mannan 1,2-(1,3)-alpha-mannosidase activity] [GO:0008496 mannan endo-1,6-alpha-mannosidase activity] [GO:0033941 mannan exo-1,2-1,6-alpha-mannosidase activity] [GO:0052766 mannoside alpha-1,4-mannosidase activity] [GO:0015924 mannosyl-oligosaccharide mannosidase activity] and see kids below.

[ukemi]

http://noctua.geneontology.org/editor/graph/gomodel:627d95ee00001794

[ukemi]

Should we request: mannan (((exo?))) 1,2-alpha-mannosidase activity [R-HSA-6799545] mannan (((exo?))) 1,3-alpha-mannosidase activity [R-HSA-8853686] mannan (((exo?))) 1,6-alpha-mannosidase activity [R-HSA-6799581] Or can we use? The referenced paper suggests yes PMID:25092655: [GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity] [GO:0004572 mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity] [GO:0052768 mannosyl-oligosaccharide 1,3-alpha-mannosidase activity] [GO:0052767 mannosyl-oligosaccharide 1,6-alpha-mannosidase activity] Does the fact that the terminal mannose links to a GlcNAC exclude the superstructure from being an oligo-mannose?

Do GO:0033941 and GO:0004572 conflate 2 molecular functions? Is mannan R-HSA-6799581 correctly annotated to endo-1,6-alpha-mannosidase activity? Shouldn't it be an exo? It doesn't seem to cleave internal to a polysaccharide chain, but rather snips off the terminal mannose.