Table 1 Performance using experimentally validated ELMs (dataset from [[14]]), searching for protein short linear motifs in disordered regions of proteins
ELM name | Number of proteins | Regular expression from ELM database | SLIMFinder with evolutionary weighting and RLC masking (Rank) | MEME default (Rank) | MEME with evolutionary weighting and RLC masking (Rank) |
|---|---|---|---|---|---|
TRG_ER_KDEL_1 | 12 | [KRH][DENQ]EL | K.{0,2}DEL$ (1) | DEL (35) | DEL (1) |
LIG_Dynein_DLC8_1 | 4 | [KR].TQT | S.K.TQT (1) | K[AESV]TQ[TE][PD] (1) | [KV][SAE]TQT 91) |
LIG_PCNA | 13 | Q.[ILM].[FHM][FHM] | [IL].S[FH]F (1) | Q.[SRT][IL][DM]SFF (1) | [LI].SFF (3) |
MOD_SUMO | 29 | [VILAFP]K.[EDNGP] | [FIV]K.E (1) | [IV]K[QE]E[PE] (1) | [IV]KEE (1) |
LIG_SH3_2 | 9 | P.P.[KR] | P.P.R.{0,1}P (1) | - | - |
LIG_CYCLIN_1 | 22 | [RK].L.{0-1}[FYLIVMP] | RR.{0,1}L.{0,1}F (1) | [GE]L[St]R[ED]L.[KE][HLR]L (5) | K[KR][KR] (1) |
LIG_CtBP | 26 | P.[DEN]L[VAST] | P[ILM]DL (1) | PLDLS (1) | PLDLS (1) |
LIG_AP_DAE_1 | 8 | [DE][DES].[F].[DE][LVIMFD] | D.F.F.S.P (1) | DDEF[GS][DE]FQ (1) | [GA]DF (1) |
LIG_14-3-3_3 | 6 | [RHK][STALV].[ST]. [PEDSIF] | S.P.S.T.P (3) | R[TS]NSA (65) | - |
LIG_RB | 25 | [LI].C.[DE] | L.C.E (6) | LVCFE (1) | - |
LIG_Clathr_ClatBox_1 | 15 | l[ILM].[ILMF][DE] | L.{1,2}DL.{0,2}D (12) | [DE][ST][NSD]l[LI][DE][LF] (9) | [LG]L[DG]LD[SG](1) |
LIG_14-3-3_1 | 4 | R[FSWY].S.P | RS.S.P (3) | RS[IPRT]S[ALMT]P (29) | S[AI]S[ALE]P (1) |
LIG_RGD | 15 | RGD | R.D.V (7) | RGD (6) | RGD (3) |
LIG_HP1_1 | 6 | P.V.[LM] | - | - | - |
LIG_NRBOX | 9 | L.LL | - | [KN]H[AKP]LLS[RN]LL[RQ] (21) | L[KRS][QY]LL (1) |
MOD_N-GLC_2 | 5 | N.C | - | [FHIMY][NS][EANS][CE][VENS] [CEHRV][VAF][MKLV][EAGS][NE] (42) | - |
TRG_lysEnd_APsAcLL | 10 | [DER]…L[LVI] | - | - | - |