Scan the indicated protein in search of glycosylation sites
gl.scan(up_id, db = 'all')
up_id a character string corresponding to the UniProt ID.
db the database where to search. It should be one among ‘PSP’, ‘dbPTM’, ‘all’.
Returns a dataframe where each row corresponds to a modifiable residue.
O-GlcNAcylation is an important post-translational modification governed by a single pair of enzymes–O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). These two enzymes mediate the dynamic cycling of O-GlcNAcylation on a wide variety of cytosolic, nuclear and mitochondrial proteins in a nutrient- and stress-responsive fashion.
The package ptm provides a function, gl.scan(), that assists in the identification of OGlcNAc sites in a given protein. The UniProt ID of the protein of interest must be passed as argument. For instance, to scan the protein vimentin, we can proceed as follows:
First, you need to search for the UniProt ID. If the protein in question is found into MetOSite, you can search the ID:
id <- meto.list('Vimentin')$prot_id id
##  "P08670"
Otherwise, go to the UniProt page to search for the ID.
## up_id organism modification database ## 1769 P08670 Homo sapiens S7-gl PSP ## 1770 P08670 Homo sapiens T33-gl PSP ## 1771 P08670 Homo sapiens S34-gl PSP ## 1773 P08670 Homo sapiens S55-gl PSP