ELM - Candidates

ELM candidate motifs

ELM annotation process is a tedious and time-consuming process involving critical reading of primary and secondary literature, finding motif instances, generating multiple sequence alignments and more. In order not to loose track of possible annotations, we keep the following list of candidate motifs.
We invite researchers to send us their feedback and expert opinion on these classes and to contribute novel motif classes that will be added to the candidate page and ultimately be turned into full ELM classes. Minimum requirements are at least one literature reference as well as a short description. In addition, a draft regular expression or a 3D structure showing the relevant interaction would also be helpful.

Currently 22 candidates need annotation: (Add a new candidate)

Detailed Status:

deleted:

Identifier	Model	References	Description	Notes	Status
LIG_PCNA_2	[ILVM][^ILVM][DHFM][ILVM]	11682605	slight variation on original PCNA motif		deleted	[Edit]
Mod_PLK_1	(.[DEN][^GP]([ST])[FILMVW]..) or (.[DEN][^GP]([ST])[^P][FILMVW].)	Alexander,2011	Revised PLK1 phosphosite based on peptide data.	Better description than the current ELM model.	deleted	[Edit]
LIG_14-3-3_4	[RHK][STALV].([ST]).[PESRDIFTQL]	17166838	Slightly modifified LIG_14-3-3_3 motif, allowing for Leucine in last position to match instance.	instance in switches.elm: SWTI000583 HAP1_RAT (P54256-2) 594 598	deleted	[Edit]
LIG_Sliding_Clamp	QL.L.[FL]	14729336	bacterial siding clamp		deleted	[Edit]
Lig_MHD_deltaCOP_1	W.{1,6}[WF]	Suckling,2015, 5FJZ	The delta-COP subunit of the Coatomer complex binds a Wx(1-6)[WF] motif in interacting proteins like Dsl1 tether (yeast) and ArfGAP1 (mammal). The motif binds to the mu homology domain of delta-COP		deleted	[Edit]
LIG_FXI_DFP_1	[FYWHIL].DFP	Wong,2016, 5EOK, 5EOD, 5I25,	The DFP motif is found in proteins, including laminins, collagen V and kininogen, that bind to an apple domain of coagulation factor XI. Depending on other properties of the DFP-containing proteins, the motif is likely to be important for localisation and/or activation of FXI		deleted	[Edit]
Mod_DYRK_RxxSP_1	Rp.[ST]P[^DEWY]..	Soppa,2015, Campbell,2002	Dual specificity tyrosine phosphorylated and regulated kinases (DYRKs) phosphorylate motifs like RpxSP. These sites cannot be recognised by other basophilic kinases due to the Pro at +1		deleted	[Edit]
LIG_REV1_RIR_1	..FF[^P]{0,2}[KR][^P]{0,4}[KR?]	Ohashi,2009, Pozhidaeva,2012, 28821613, 2N1G, 2LSI, 2LSK, 2LSJ, 4GK5	The RIR motif is found in DNA repair proteins including XRCC1, Pol-Eta, -Iota, -Kappa and -Zeta. The motif binds the C-terminal domain of the modular protein REV1 which catalyses deoxycytidyl transfer to the 3’ end of a DNA primer.	The motif has two core phenylalanine residues which initiate an alpha-helix: Their backbone peptide groups make electrostatic interactions to an Asp residue in Rev1. The remainder of the helix has one or more semi-conserved basic residues interacting with acidic residues on the Rev1 surface. The aromatic residue pair and basic amino acid preference is similar to PIP Box and MIP box and some motifs might overlap.	deleted	[Edit]
DOC_PP2B_PxIxI_2	.P.LP[IL].	xx	xx		deleted	[Edit]
LIG_VCP_VBM_2		[MILVAK][RK][^P][^P]R[LFWE][^P][^P][FLI][^P]	Lim,2016 18208387 5EPP	Helical motif binding a groove in the N-terminal domain of the VCP/P97/Segregase ATPase involved in transitional ER formation and other processes including ubiquitin-proteasome targeting. The VIM motif binds the same pocket in reverse orientation.	deleted	[Edit]
LIG_SH2_SRC11	P[KR]	123123	hello	hello	deleted	[Edit]
LIG_SH2_SRC1	TTT	123123	123safd	sadfsafd	deleted	[Edit]
LIG_SH2_SRC3	P..P[KR]T	123123	lkjss	lkjsdf	deleted	[Edit]
LIG_KLC1	[ILMV].WD..	Konecna,2006	motif mediating binding to the tetratricopeptide repeats of KLC1	duplicate of LIG_KLC1_TPR_1	deleted	[Edit]
LIG_Wnt	LT...W	Umbhauer,2000	Motif found in Frizzled (Receptor of Wnt) and involved in the activation of the Wnt/beta-catenin signaling pathway. Mutations in the fixed positions induce the expression of the Wnt target gene siamois.	see LIG_Fzd_KTXXXW	deleted	[Edit]
LIG_APCC_KILR	KILR	Izawa,2012	Motif in Cdc20 that mediates binding to APC/C subunits. The main determinants are the I and L residues; mutation of the basic residues decreases but not abrogates binding to both APC/C and Mad2. This same sequence also mediates binding of Cdc20 to Mad2 (see LIG_MAD2); preventing the motif to bind APC/C by hiding by Mad2 would be one of several mechanisms involved in regulation of APC/C activity and substrate specificity by the spindle assembly checkpoint.	Possible interactor is Cdc23 TPR region, see Matyskiela,2009.	deleted	[Edit]
LIG_VHS	D..LL	20502673 1ELK 10985773	The VHS domain of GGA proteins binds to an acidic di-leucine motif in the cytoplasmic domain of sorting receptors including the mannose 6-phosphate receptor.	duplicate of TRG_LysEnd_GGAAcLL_1	deleted	[Edit]
LIG_BCL2	L..I[AG]D.[ILV]	20502673 1BXL Sattler,1997	Bcl2 motif		deleted	[Edit]
LIG_HIV1-GP41	H..NPF	16904109	HIV-1 gp41 core-binding motif.		deleted	[Edit]
CLV_C14_Caspase-8-10	[^RK][EDQ].D	1221285 1236692 19694615 10964557 10508785	Caspase-8 and -10 are the initiator caspase in the extrinsic apoptotic pathway and cleaves executor caspases.	Motif suggestion is based on in vitro data. Optimal described sequence is LETD. For protein substrate see MEROPS or CutDB No in vitro data for caspase-10 but cleavage motif LEXD in literature is described.	deleted	[Edit]
LIG_CD40	EQLKKSKTL	21998326	Linear peptide in an exposed loop mediates interaction between CD40L and Mac-1	might be too specific paper not freely accessible	deleted	[Edit]
LIG_PTB_splicing	[SG][IL]LG..P	Rideau,2006	Motif essential for splicing repressor activity found in cofactors of the PTB regulatory splicing repressor (Polypyrimidine tract-binding protein).		deleted	[Edit]

Please cite: ELM-the Eukaryotic Linear Motif resource-2024 update. (PMID:37962385)

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