Scans the indicated protein in search of S-nitrosylation sites
up_id a character string corresponding to the UniProt ID.
Returns a dataframe where each row corresponds to a modifiable residue.
Huang et al. Nucleic Acids Res. 2019 47:D298-D308.
S-Nitrosylation is the covalent attachment of a nitric oxide group (-NO) to cysteine thiol within a protein to form an S-nitrosothiol (SNO). S-nitrosylation has diverse regulatory roles in bacteria, yeast and plants and in all mammalian cells.
The package ptm provides a function, sni.scan(), that assists in the identification of S-nitrosylation 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 ## 4138 P08670 NA C328-Sni dbPTM