proteinModification [pmod] v.2.1.0 (current)

Long form: proteinModification() Short form: pmod()

The proteinModification() or pmod() function can be used only as an argument within a proteinAbundance() function to indicate modification of the specified protein. Multiple modifications can be applied to the same protein abundance. Modified protein abundance term expressions have the general form:

p(ns:protein_value, pmod(ns:type_value, <code>, <pos>))

type_value (required) is a namespace value for the type of modification , ** (optional) is a single-letter or three-letter code for one of the twenty standard amino acids, and (optional) is the position at which the modification occurs based on the reference sequence for the protein. If ** is omitted, then the position of the modification is unspecified. If both ** and ** are omitted, then the residue and position of the modification are unspecified. NOTE - the default BEL namespace includes commonly used protein modification types.

Additional modification types can be requested as needed, or an external vocabulary can be used. Like other BEL namespace values, these modification types can be equivalenced to values in other vocabularies.

Protein Modification Default Namespace

Label Synonym
Ac acetylation
ADPRib ADP-ribosylation, ADP-rybosylation, adenosine diphosphoribosyl
Farn farnesylation
Gerger geranylgeranylation
Glyco glycosylation
Hy hydroxylation
ISG ISGylation, ISG15-protein conjugation
Me methylation
Me1 monomethylation, mono-methylation
Me2 dimethylation, di-methylation
Me3 trimethylation, tri-methylation
Myr myristoylation
Nedd neddylation
NGlyco N-linked glycosylation
NO Nitrosylation
OGlyco O-linked glycosylation
Palm palmitoylation
Ph phosphorylation
Sulf sulfation, sulphation, sulfur addition, sulphur addition, sulfonation, sulphonation
Sumo SUMOylation
Ub ubiquitination, ubiquitinylation, ubiquitylation
UbK48 Lysine 48-linked polyubiquitination
UbK63 Lysine 63-linked polyubiquitination
UbMono monoubiquitination
UbPoly polyubiquitination

Supported One- and Three-letter Amino Acid Codes

Amino Acid 1-Letter Code 3-Letter Code
Alanine A Ala
Arginine R Arg
Asparagine N Asn
Aspartic Acid D Asp
Cysteine C Cys
Glutamic Acid E Glu
Glutamine Q Gln
Glycine G Gly
Histidine H His
Isoleucine I Ile
Leucine L Leu
Lysine K Lys
Methionine M Met
Phenylalanine F Phe
Proline P Pro
Serine S Ser
Threonine T Thr
Tryptophan W Trp
Tyrosine Y Tyr
Valine V Val

Function Signatures

proteinModification(StrArgNSArg, StrArgNSArg?, StrArg?)
  1. Namespace argument or default namespace argument (without prefix) of following type(s): ProteinModification

  2. Zero or one amespace argument or default namespace argument (without prefix) of following type(s): AminoAcid

  3. Zero or one string argument of following type(s): /\d+/


default BEL namespace and 1-letter amino acid code

p(HGNC:AKT1, pmod(Ph, S, 473))

default BEL namespace and 3-letter amino acid code

p(HGNC:AKT1, pmod(Ph, Ser, 473))

PSI-MOD namespace and 3-letter amino acid code

p(HGNC:AKT1, pmod(MOD:PhosRes, Ser, 473))

MAPK1 phosphorylated at both Threonine 185 and Tyrosine 187

p(HGNC:MAPK1, pmod(Ph, Thr, 185), pmod(Ph, Tyr, 187))

HRAS palmitoylated at an unspecified residue using default BEL namespace

p(HGNC:HRAS, pmod(Palm))

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