gl.scan()

Description

Scan the indicated protein in search of glycosylation sites

Usage

gl.scan(up_id, db = 'all')

Arguments

up_id a character string corresponding to the UniProt ID.
db the database where to search. It should be one among ‘PSP’, ‘dbPTM’, ‘all’.

Value

Returns a dataframe where each row corresponds to a modifiable residue.

References

Hornbeck et al. Nucleic Acids Res. 2019 47:D433-D441.
Huang et al. Nucleic Acids Res. 2019 47:D298-D308.

See Also

ac.scan(), meto.scan(), p.scan(), me.scan(), ub.scan(), su.scan(), dis.scan(), sni.scan(), ni.scan(), ptm.scan(), reg.scan()

Details

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

## [1] "P08670"

Otherwise, go to the UniProt page to search for the ID.

Then,

gl.scan(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