Description
Renumerates residue position of a MetOSite sequence to match the corresponding UniProt sequence
Usage
renum.meto(uniprot)
Arguments
uniprot the UniProt ID.
Value
Returns a dataframe containing the re-numerated sequence.
See Also
aa.at(), is.at(), aa.comp(), renum.pdb(), renum()
Dependencies
To use this function you will need MUSCLE installed in your computer.
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:
On a few occasions the numeration of the sequences coming from UniProt and MetOSite don’t fully match. For instance, the sequence given in MetOSite may be the one corresponding to the mature form of the protein (because the numeration use in the literature is that for the mature form) and the sequence found in UniProt may be that of the precursor protein. When this happens it is useful to have a tool such as renum.meto() that will re-numerate the residues for us.
Let’s see an example using the protein alpha-1-antitrypsin as model. The mature form of the protein (sequence given by MetOSite) is formed by proteolytic cleavage of a precursor (sequence given by UniProt). Thus, the processed protein starts at the position 25 from the precursor.
up_meto <- renum.meto('P01009')
kable(up_meto[1:35, ])
| aln_pos | uni_pos | uniprot | meto | meto_pos | meto_renum |
|---|---|---|---|---|---|
| 1 | 1 | M | – | NA | NA |
| 2 | 2 | P | – | NA | NA |
| 3 | 3 | S | – | NA | NA |
| 4 | 4 | S | – | NA | NA |
| 5 | 5 | V | – | NA | NA |
| 6 | 6 | S | – | NA | NA |
| 7 | 7 | W | – | NA | NA |
| 8 | 8 | G | – | NA | NA |
| 9 | 9 | I | – | NA | NA |
| 10 | 10 | L | – | NA | NA |
| 11 | 11 | L | – | NA | NA |
| 12 | 12 | L | – | NA | NA |
| 13 | 13 | A | – | NA | NA |
| 14 | 14 | G | – | NA | NA |
| 15 | 15 | L | – | NA | NA |
| 16 | 16 | C | – | NA | NA |
| 17 | 17 | C | – | NA | NA |
| 18 | 18 | L | – | NA | NA |
| 19 | 19 | V | – | NA | NA |
| 20 | 20 | P | – | NA | NA |
| 21 | 21 | V | – | NA | NA |
| 22 | 22 | S | – | NA | NA |
| 23 | 23 | L | – | NA | NA |
| 24 | 24 | A | – | NA | NA |
| 25 | 25 | E | E | 1 | 25 |
| 26 | 26 | D | D | 2 | 26 |
| 27 | 27 | P | P | 3 | 27 |
| 28 | 28 | Q | Q | 4 | 28 |
| 29 | 29 | G | G | 5 | 29 |
| 30 | 30 | D | D | 6 | 30 |
| 31 | 31 | A | A | 7 | 31 |
| 32 | 32 | A | A | 8 | 32 |
| 33 | 33 | Q | Q | 9 | 33 |
| 34 | 34 | K | K | 10 | 34 |
| 35 | 35 | T | T | 11 | 35 |
We can see that the function renum.meto() has renumerated all the residues from the MetOSite sequence to force them matching the UniProt numeration.
