Description
Scans the indicated protein in search of sumoylation sites
Usage
su.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(), ni.scan(), gl.scan(), ub.scan(), sni.scan(), dis.scan(), ptm.scan(), me.scan(), p.scan(), reg.scan()
Details
Protein sumoylation The post-translational modification by sumoylation is a major regulator of protein function that plays an important role in a wide range of cellular processes.
The package ptm provides a function, su.scan(), that aims to integrate information from different PTM databases, and assist to identify sumoylation sites in a given protein. The UniProt ID of the protein of interest must be passed as argument. A second argument for this function is db, used to indicate the database to be searched. The databases accessible for this purpose are:
By default, su.scan() use all above databases to search for sumoylation sites. In this case, it should be noted that the same sumoylation site can appear twice if it is present in both databases. If we wish to get a list of unique sumoylation sites found, for instance, in the protein Histone H3.1t, 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('Histone H3.1t')$prot_id
id
## [1] "Q16695"
Otherwise, go to the UniProt page to search for the ID.
Then,
unique(su.scan(id)$modification)
## [1] "K15-sm" "K57-sm" "K80-sm" "K123-sm"
ptm 