aa.at()

Description

Returns the residue found at the requested position

Usage

aa.at(at, target, uniprot = TRUE)

Arguments

at the position in the primary structure of the protein.

target a character string specifying the UniProt ID of the protein of interest or, alternatively, the sequence of that protein.

uniprot logical, if TRUE the argument ‘target’ shoud be an ID.

Value

Returns a single character representing the residue found at the indicated position in the indicated protein.

See Also

is.at(), renum.pdb, renum.meto(), renum()

Details

The ptm package offers a set of ancillary functions aimed to carry out rutinary work, which may be needed when more elaborated analysis are required. Among these ancillary function are:

The function aa.at() returns the amino acid found at the requested position of the target sequence. For instance, if we want to know what amino acid is found at the position 100 of the horse cytochrome c (P00004):

aa.at(100, 'P00004')


## [1] "K"

We can afirm that the amino acid found is a lysine (K).

The target sequence doen’t need to be a UniProt sequence, it can be any string of amino acid, in that case we should pass the argument uniprot = FALSE:

aa.at(at = 10, target = "GDVEKGKKIFVQKCAQCHTVEKGGK", uniprot = FALSE)


## [1] "F"

In this case, at the position 10 of the string that we have passed as argument, we find a phenylalanine (F).

We have found this function to be useful to carry out data quality controls. For instance, if we carry out a query in MetOSite (a database for sulfoxidation sites), asking for the protein alpha1-antitrypsin (P01009), we obtain:

meto.scan('P01009')$Metosites[[1]]


## [1] "351" "358" "385"

To verify that there was no error with the annotations, we checked that indeed methionine residues are found at this positions:

lapply(as.numeric(meto.scan('P01009')$Metosites[[1]]), 
       function (x) aa.at(x, get.seq('P01009', db = 'metosite'), uniprot = FALSE))


## [[1]]
## [1] "M"
## 
## [[2]]
## [1] "M"
## 
## [[3]]
## [1] "M"