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Table 1 Performance using experimentally validated ELMs (dataset from [[14]]), searching for protein short linear motifs in disordered regions of proteins

From: Profile-based short linear protein motif discovery

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] - - -
  1. All proteins contain at least one experimentally determined motif instance. The regular expression that matches the annotated ELM regular expression is returned for each method along with its rank (in brackets). No result is indicated by a dash. Niall Haslam 24 October 2012 09:18.