Table 3.
Short Linear Motifs (SLiM) description.
| ELM Class Identifier | Regular Expression | Interaction Partner(s) | Examples of Proteins * Containing the SLiM |
|---|---|---|---|
| DEG_Nend_ UBRbox_3 | ^M{0,1}([NQ]) | Aminohydrolases for deamidation | - |
| DOC_WW_Pin1_4 | ...([ST])P. | Peptidyl prolyl isomerase 1 | Many |
| LIG_FHA_1 | ..(T)..[ILV]. | Proteins containing the forkhead-associated domain, e.g., TIFA, TIFAB, AGGF1 | Kinesin interactors, TIFA |
| LIG_IBAR_NPY_1 | NPY | I-BAR domain-containing proteins, involved in membrane dynamic | The bacterial protein Tir, SHANK2 |
| LIG_PDZ_Class_3 | ...[DE].[ACVILF]$ | PDZ containing proteins, PDZ domains also bind to phospholipid headgroups | Many PDZ ligands are membrane proteins |
| LIG_PTB_Apo_2 LIG_PTB_Phospho_1 |
(.[^P].NP.[FY].)|(.[ILVMFY].N..[FY].) (.[^P].NP.(Y))|(.[ILVMFY].N..(Y)) |
Proteins containing phosphotyrosine binding (PTB) domains, e.g., insulin receptor substrate 1 (IRS-1) | Integrins, LRP1 |
| LIG_SH2_CRK | (Y)[^EPILVFYW][^HDEW][PLIV][^DEW] | Proteins containing SH2 domain of the CRK family | Transmembrane receptors, Phospholipase C-gamma-1 |
| LIG_SH2_NCK_1 | (Y)[DESTNA][^GWFY][VPAI][DENQSTAGYFP] | Proteins containing SH2 domain of the NCK family | Transmembrane proteins, adapter protein docking 1 |
| LIG_SH2_STAP1 | (Y)[DESTA][^GP][^GP][ILVFMWYA] | Proteins containing SH2 domain of the STAP1 family | Transmembrane proteins, lipid phosphatase |
| MOD_CDK_SPK_2 | ...([ST])P[RK] | Cyclin-dependent kinases, proline directed kinase | Proteins involved in different biochemical pathways |
| MOD_GSK3_1 | ...([ST])...[ST] | Glycogen synthase kinase 3, needs priming, inhibitory | |
| MOD_NEK2_1 | [FLM][^P][^P]([ST])[^DEP][^DE] | Never in mitosis A (NimA)-related kinases | |
| MOD_PKA_1 | [RK][RK].([ST])[^P].. | cAMP-dependent protein kinase A, basophilic kinase | |
| MOD_ProDKin_1 | ...([ST])P.. | MAP Kinase, proline directed kinase |
* Proteins involved in lipid metabolism, inflammation, redox reactions, lipid transfer, or in membrane complexes.