Modification abbreviation
From ReactomeWiki
Naming Entities with modified residues
Modified residue abbreviations
- Phosphorylated residue: p-
- ubiquitinated residue: ub-
Format of name with modified residue
Rules for representing phosphorylation and other residue modifications in entity names
1. For phosphorylations, use lowercase p followed by a dash at the beginning of the name, e.g. p-ENTITYNAME
2. Phosphorylation at an unknown position in the peptide sequence should still represent the residue type if known, otherwise use the p-prefix only, e.g. for a tyrosine phosphorylation at an unknown position use p-Y-ENTITYNAME, for a phosphorylation at unknown position and residue type use p-ENTITYNAME.
3. If known, represent the position of the phosphorylated residue in the reference entity peptide sequence as a number after the residue, e.g. p-Y244-ENTITYNAME. Always refer to the reference entity, not the residue numbering used in publications or numbering from the start of the mature peptide.
4. When an entity is phosphorylated more than once at known positions, represent the multiple residues in the order they occur in the primary peptide sequence, e.g. p-Y35,S188,Y601-ENTITYNAME. No spaces around the commas.
5. A maximum of 4 residue positions can be given. If greater than 4, use a number in front of the phosphorylated residue type to indicate the number of occurrences, e.g. p-4Y-ENTITYNAME, or p-2S,2Y-ENTITYNAME.
6. When some positions are known but others are unknown, represent the unknown positions first, e.g. pS,Y345-ENTITYNAME
7. When naming a set, where the members are serine or threonine phosphorylated at the same conserved position in the sequence, it is acceptable to use p-(S/T)345-SETNAME.
8. When combining more than one modification type, separate them using dash, e.g. for a protein that is ubiquitinated at position 47 and serine phosphorylated at position 103 , Ub-K47-pS103-ENTITYNAME.