Modified Forms Described in the BKL
Notation for Modified Forms in the BKL
A protein can be modified by covalent binding of various groups to one or more amino acid residues, by complexing with other proteins, or by a change in the location of the protein. A protein can also exist in an unmodified form. The general notation used to describe various modified forms of BKL Molecules is shown in the table below, with the notation appended to the Molecule name. Modified Forms appear on the Locus Report, on the Protein view.
BKL Modified Form Notation
| Notation | Meaning |
|---|---|
| {mod} | Indicates a covalently modified form. Types of modifications described in the BKL are shown in the table below. |
| {mod}n | Indicates that the Molecule exists in a state with multiple modifications, where n can be any number. Hyperphosphorylation is a modified state and can be indicated as {p}2, for example. |
| {mod(n)} | Indicates that the Molecule exists in a state with multiple modifications of a single residue, where n can be any number. Polyubiquitination at lysine residue 145 is an example of such a modified state and can be indicated as: {ub(4)K145}. |
| {modAAposition} | Indicates that a Molecule is modified in a specific way, at a specific residue. Phosphorylation of serine residue 175 and tyrosine residue 53, for example, can be indicated as: {pS175}{pY53}. |
| A:B:C | Indicates that a Molecule is in a complex with another Molecule or Molecules. For example, a complex of human p53 with human Mdm2 is indicated as: Mdm2(h):p53(h). A complex of phosphorylated human Mdm2 and human p53 is indicated as: Mdm2(h){pS269}:p53(h). |
Types of Modifications in the BKL
Many modifications are described in the BKL. Abbreviations for these modifications are explained in the table below.
Modifications Described in the BKL
| Abbreviation | Meaning |
|---|---|
| {ace} | Acetylated |
| {acyl} | Acylated |
| {ade} | Adenylated |
| {ami} | Amidated |
| {biot} | Biotinylated |
| {car} | Carboxylated |
| {chol} | Cholesterol modified |
| {cit} | Modified with citrulline (derived from methylated arginine) |
| {cl} | Cross-linking, e.g. {clCC57,146} -> crosslinked AA and their chain positions |
| {deca} | Decanoylated |
| {drib} | ADP ribosylated |
| {elon} | Conjugated with elongin B |
| {far} | Farnesylated |
| {fuc} | Fucosylated |
| {gal} | Galactosylated |
| {ger} | Geranylgeranylated |
| {glu} | Glucosylated |
| {glugal} | Glucosylgalactosylated |
| {glut} | S-glutathionylated |
| {gly} | Glycosylated |
| {H+} | Protonated residue |
| {hyd} | Hydroxylated |
| {hyd3} | Conversion to 3-hydroxy |
| {hyd4} | Conversion to 4-hydroxy |
| {hyd5} | Conversion to 5-hydroxy |
| {isg} | ISGylated; conjugation with ISG15 |
| {lipo} | Lipoylated |
| {man} | Mannosylated |
| {met} | Methylated |
| {mod} | Undefined modification |
| {myr} | Myristoylated |
| {nedd} | Neddylated (conjugated with Nedd8) |
| {no} | Nitrosylated |
| {no2} | Nitrated |
| {octa} | Octanoylated |
| {ox} | Oxidized (For example, describes cysteine residues that are intramolecularly linked via a disulfide bridge in the oxidized protein, and the bridge is disconnected in the reduced form.) |
| {p} | Phosphorylated |
| {pant} | O-phosphopantetheine modification |
| {pal} | Palmitoylated |
| {pole} | Polyglutamylated |
| {polg} | Polyglycylated |
| {pren} | Prenylated |
| {pyp} | Pyridoxal phosphate modification |
| {re} | Reduced |
| {ret} | All-trans-retinyl group |
| {reti} | Retinylidene |
| {soh} | Sulfenylated |
| {sol} | Soluble |
| {sox} | Sulfur oxygenated |
| {sul} | Sulfated |
| {sumo} | Sumoylated (conjugated with SUMO-1) |
| {sumo2} | Sumoylated (conjugated with SUMO-2) |
| {sumo3} | Sumoylated (conjugated with SUMO-3) |
| {U} | Conversion to selenocysteine |
| {ub} | Ubiquitinated |
| {xyl} | Xylosylated |
| {Y} | Converted to tyrosine residue |
| {gal|glu|fuc|xylAA(CHEBI:ID)} | To differentiate between diverse sugar chains at glycosylated or galactosylated residues, a reference to a CHEBI database entry is given in parentheses |