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Table 2 Most used SLiMs conserved and located in HIV-1 disordered regions

From: Prediction of virus-host protein-protein interactions mediated by short linear motifs

SLiM #HIV-proteins Pfam domain Domain name
LIG_WD40_WDR5_VDV_2 17 IPR017986 WD40-repeat-containing domain
DOC_USP7_1 17 PF00917 MATH domain
CLV_NRD_NRD_1 16 PF00675 Insulinase (Peptidase family M16)
CLV_PCSK_KEX2_1 15 PF00082 Peptidase_S8 Subtilase family
MOD_GSK3_1 15 PF00069 Protein kinase domain
MOD_PIKK_1 15 PF00454 Phosphatidylinositol 3- and 4-kinase
CLV_PCSK_SKI1_1 14 PF00082 Peptidase_S8 Subtilase family
LIG_SH3_3 14 PF00018 SH3 domain
MOD_NEK2_1 13 PF00069 Protein kinase domain
LIG_FHA_2 13 PF00498 FHA domain
MOD_CK1_1 13 PF00069 Protein kinase domain
LIG_FHA_1 12 PF00498 FHA domain
DOC_CYCLIN_1 12 PF00134 Dynein light chain type 1
LIG_LIR_Nem_3 12 PF02991 Autophagy protein Atg8 ubiquitin like
DOC_WW_Pin1_4 12 PF00397 WW domain
MOD_ProDKin_1 12 PF00069 Protein kinase domain
MOD_PKA_2 12 PF00069 Protein kinase domain
MOD_CK2_1 12 PF00069 Protein kinase domain
TRG_ER_diArg_1 12 PF00400 WD domain, G-beta repeat
LIG_SH2_STAT5 11 PF00017 SH2 domain
LIG_LIR_Gen_1 11 PF02991 Autophagy protein Atg8 ubiquitin like
CLV_PCSK_PC1ET2_1 11 PF00082 Peptidase_S8 Subtilase family
MOD_GlcNHglycan 11 PF01048 Phosphorylase superfamily
MOD_N-GLC_1 10 PF02516 Oligosaccharyl transferase STT3 subunit
TRG_ENDOCYTIC_2 10 PF00928 Adaptor complexes medium subunit family
  1. From the SLiMs that are conserved in more than 70% of the HIV-1 protein sequences, and are located in disordered regions too we counted how many HIV-1 proteins include them. In this table we report the SLiMs more commonly used in HIV-1 proteins, the ones that are included in 10 or more of the HIV-1 proteins. The table includes the counter domain for every SLiM