The Eukaryotic Linear Motif resource for
Functional Sites in Proteins

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 232 candidates need annotation: (Add a new candidate)

Detailed Status:
first draft: 232
Identifier Model References Description Notes Status
MOD_CAAXbox_2 (C)[^DEQ][LIVMF].$ 20813839, 15710609, 17411337 Two bacterial instances (SifA from Salmonella and Lpg1976 from Legionella) are experimentally validated Prenylation motifs. However, they slightly differ from the canonical ELM MOD_CAAXbox. The in silico predictor PrePS recognizes this extended regular expression. first draft
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LIG_14-3-3_5 IRLNNAIWRAWY Ge,2012,Sato,2016
A newly identified 14-3-3 binding motif identified in ChREBP protein. Unlike other 14-3-3 binding proteins, here 14-3-3 binds to a non-phosphorylated site in ChREBP with high affinity and the interaction can be activated by a free sulfate or phosphate molecules provided by the metabolites like AMP or ketone bodies.AMP binds directly to ChREBP and allosterically induces conformational changes resulting in increased affinity of ChREBP for 14-3-3and stabilization of the heterodimer in the cytoplasm of hepatocytes thus inhibiting fat synthesis during periods of ketosis. The main interaction interaction interface is between the α2 helix of the ChREBP and the positively charged patch containing a Arg-Arg-Tyr triad on the binding groove on 14-3-3. Motif is highly conserved in mammals. first draft
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RTX_motif G..G.[DN].[LVIFY]. 19015266
27058787
17728256
8253063
This motif is present in several bacterial toxins, usually in 5 to 50 repeats, and are highly common in effector proteins from the type one secretion system (T1SS) (19015266).

In CyaA from Bordetella pertussis, the motifs are located in a predominantly disordered region at the C-terminal of the protein. Under nanomolar concentrations of Ca2+ (as in the bacterial cytosol) the C-terminal region lacks a terciary and secondary structures. After CyaA is transported through the T1SS, the protein gets in contact with Ca2+ which is sequestered and induces the folding of CyaA into β-Rolls Ratchets (27058787).

The motif has also been described in extracellular lipase from Serratia marcescens (2QUA; 2QUB), Serralysin from Pseudomonas aeruginosa, triacylglycerol lipase from P. aeruginosa (1EX9), Hemolysin from Escherichia coli, triacylglycerol lipase from Brukholderia cepacia (1OIL) and in the fungal lipase from Thermomyces lanuginosus (1EIN; 1DT3) (17728256; 8253063).
CyaA has PDB structures: 5CVW and 5CXL first draft
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LIG_Vh1_VBS_2 DD[VMIL][MILFYPA].[TASKHCR][AVSCT]..[ILVM]...[LMTVI]..[LMV][ILVMAT]..[AIVLMT] Park,2011 Surface cell antigen 4 (sca4) is a protein from R. rickettsii that contains two VBSs, sca4-VBS-N and sca4-VBS-C, where the former resembles the binding of the talin or IpaA VBSs The later contains a Pro at position +14 causing a kink in the helix structure. The crystal structure of sca4-VBS-C with vinculin (3TJ6) shows that the position of the alpha-helix alpha1 in the Vh1 domain of vinculin has a dramatic movement compared to its corresponding position in other structures containing non-kinked helices (Park,2011), therefore exemplifying a new variant of a Vh1 binding-motif. first draft
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TRG_ER_KDEL_2 [KRHQSAP][DENQT][ED]L[K]{0,1}$ 9914159 Same as previous TRG_ER_KDEL_1 but modified to recognize the C-terminal motif in Exotoxin A in Pseudomonas as well as its closely related species. The Lys at the C-terminal position is conserved in all Exotoxin As from P. aeruginosa as well as in Cholix toxin from V. cholerae.

The position -3, counting from the C-terminal, in Exotoxin A from P. aeruginosa has a conserved Asp while all the Cholix toxins have a Glu.

An exotoxin from Aeromonas hydrophila does not contain the same Lys at the last position (resembling the canonical KDEL motif) but half of the sequences (11 out of 26) have an Asp at the position -2 counting from the C-terminal.
first draft
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LIG_IBAR_NPY_1 NPY 16922867 The binding site in Tir to induce EspFU-dependent actin assembly was mapped to a 12 aas region which is necessary and sufficient to recruit EspFU and initiate actin pedestal formation.

17521329 Defined the motif NPY as responsible for pedestal formation when present in a Tir protein (either EHEC or EPEC). Its function is EspFU-dependent.

19286134 IRSp53 links the enterohemorrhagic E. coli effectors Tir and EspFU for actin pedestal formation.

19366662 IRTKS links the EHEC actin assembly effectors Tir and EspF(U) during pedestal formation. WASP, EspFU and IRTKS-SH3 domain forms a complex.

21893288 Got the structure of EHEC Tir and the I-BAR domains of IRSp53 (2YKT). All residues contacting the NPY motif are conserved in IRSp53 and IRTKS.
Some pathogens have developed infection mechanisms that hijack host cell signalling so that they can extend their survival and satisfy their metabolic needs. Enterohemorrhagic Escherichia coli (EHEC) and Enteropathogenic E. coli (EPEC) interfere with the regulation of actin polymerization to ultimately form an actin pedestal that probably increases the contact area between the infected cell and the bacteria.

To do so, two slightly different mechanisms are used by EHEC and EPEC. Initially, the translocated intimin receptor (Tir) is traslocated by the type III secretrion system (T3SS). The Tir protein contains one globular cytoplasmic N-terminal domain that is dispensable for the pedestal formation but regulates its length (16922867), one central and extracellular domain that mediates binding to the bacterial intimin protein and a C-terminal domain that differs in the different pathovars. EPEC Tir contains a short insertion around Tyr 474 that is phosphorylated by host cell kinases and works as a binding motif (LIG_SH2_SRC) for the SH2 domain in Nck proteins. Nck, recruited to the plasma membrane and in particular close to the bacterial attachment site, activates N-WASP by using its LIG_GBD_Chelix_1 motif to bind to the GBD domain of N-WASP. The VCA regions can, then, activate Arp2/3 and initiate actin polimerization leading to pestestal formation.

EHEC Tir lacks the Nck binding property, instead, it sequesters and activates N-WASP by a ternary complex that includes a second effector protein, EspFU, and the host proteins IRSp53 or IRTKS. EHEC Tir uses the NPY motif located at the C-terminal domain to bind to the I-BAR domain of IRSp53/IRTKS (16922867; 17521329; 19286134; 19366662; 21893288). IRSp53/IRTKS has an SH3 domain that interacts with the multiple LIG_SH3_3 motif in EspFU. EspFU, in addition, has a LIG_GBD_Chelix_1 that mimics the same motif in Nck then converging in the activation of actin polymerization and pedestal formation with EPEC.
Based on the alignment of EHEC Tir proteins, the Ala at position +4 is conserved in EHEC Tir and EPEC Tir homologs as well as in putative intimin receptors in Edwarsiella and not in Lactobacilus aquaticus that has a Val at +4.
The Ala at position +4 faces opposite to the I-BAR domain in the 2YKT structure.

Position -1 is not conserved and varies in homologs (Val EHEC, D/E EPEC).

Position -2 has a conserved Val in all Escherichia spp. homologs and a Leu in Edwardsiella homologs. The Val fits in a non-hydrophobic pocket. Mutation of this Val to Ala did not affect pedestal formation (17521329). The pocket is made by Arg114 and Tyr115.

Supplementary Table 3 from de Groot (21893288) contains possible NPY-containing interactors of I-BAR:
Only LIMK1 and LIMK2 had Val in position -2. Only MYO15 had Ala in position +4.
These proteins matched with the MEME logo generated with the EHEC and EPEC Tir homologs and putative intimin receptors: ITSN1, ITSN2 and SHAN2 (SHANK2).
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LIG_IRF3_1 [DEN]L.I(S)|[DE]{2}.[DE]L.IS Zhao,2016 Structural and functional studies about the pLxIS motif in cellular and viral proteins. Structures of STING (5JEJ), MAVS (5JEK), TRIF (5JEK) and NSP1 (5JEO; 5JER) with IRF-3. Structure of the IRF-3 dimer (5JEM).
Liu,2015 Phosphorylation of the pLxIS motif.
Barro,2005 The C-terminal region of NSP1 binds IRF-3 and mediates its degradation.

The recognition of pathogen-associated molecular patters (PAMPs) involves different pathways that can trigger convergent antimicrobial responses. Microbial double-stranded (ds)DNA in the cytosol is sensed by cGAS whcih produces the second messenger cGAMP, cGAMP binds to the adaptor protein STING which is located at the endoplasmic reticulum (ER) surface. Viral dsRNA is sensed in the cytosol by RLRs which activates the adaptor protein MAVS which is located at the mitochondria surface. Membrane anchored toll-like receptors (TLRs) 3 and 4, which recognize viral dsRNA and bacterial LPS, respectively, when activated recruit the adaptor protein TRIF. The three adaptor proteins STING, MAVS and TRIG contain a conserved motif previously refered as pLxIS that is phosphorylated by TBK1 or IKKepsilon (Liu,2015). Once phosphorylated, it binds to the transcription factor IRF-3 resulting in TBK1-dependent phosphorylation of an additional pLxIS motif in IRF-3. Phosphorylated IRF-3 forms a dimer that activates the protein (Zhao,2016). IRF-3 dimer translocates to the nucleus and positively regulates the trasncription of IFN-beta (Honda,2006).

Interestingly, rotavirus is able to escape innate immune recognition by interfering with the IRF-3-dependent pathway. The rotavirus E3 ubiquitin ligase nonstructural protein 1 (NSP1) also contains the pLxIS motif which binds to the same binding region in IRF-3 in an unphosphorylated manner preventing its activation and promoting its degradation.
In STING, the Pro at position -1 is conserved in mamals and reptiles. Leu is present in birds, opossum has a Thr at position +5.

In MAVS, the motif is only conserved in mammals. Birds and fish do not have it. Tasmania devil has RLLIS. Ornithorhynchus has RLDMS and a DLNIS at 280-284. Nestor notabilis (bird) has a DLYIS at 269-273. Dipodomys (kangaroo rat) has a small duplication in the motif: EDLAISPSSSLscsEDLAISPSSSL.

In TRIF, the human instance is NLEIS, which is present in 29 species in the alignment, including four legged mammals, bats and wild ducks. 12 sequences have HL.IS including primates, panda, mus musculus and fish. Other mammals had Ser, Ala, Glu, Val and Lys. Ser at position +5 was conserved in Mammals, reptiles, birds and fish. The lizard Anolis has HLEIS at 344-348. Birds have a Phe at position +2.

In IRF-3, the motif is conserved in Mammals, reptiles, fish. Common marmoset (new world monkey), ginea pig, bats and european polecat have RLQIS. Tetraodon nigroviridis (fish) has SLQIS. The common marmoset, ginea pig, bat and the european polecat have DLLIS at ~227-231. Tetrodon nigrovorans has DLEIS at 209-213.

In NSP1, the phosphorylation is not necessary. Substitution of Ser at position +5 did not abolish the targeting of IRF-3, however it is conserved. L486A (position +2) abolished the activity of NSP1. I488A (position +4) partially impairs the activity of NSP1.
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LIG_GBD_Chelix_1 [ILV][VA][^P][^P][LI][^P][^P][^P][LM] Kim,2000 NMR structure of autoinhibited human WASP (1EJ5).
15235593 NMR structure of human WASP with a small molecule inhibitor (1T84).
17893247 EspF from EPEC can bind to N-WASP as proved by coimmunoprecipitation assays and in vitro Arp2/3 activation. They measured the Kd for EspF and mini-N-WASP/Arp2/3 =11.8 nM.
Cheng,2008 EspFU activates WASP (NMR structure 2K42).
Sallee,2008 Alanine scan in rat N-WASP and human WASP and defined the main contacting residues. Effect on multiple binding of the repeats in EspFU.
22921828 NMR structure of the 3-proteins complex: human N-WASP, the SH3 domain of human IRTKS (aka BAIAP2L1) and one repeat of EspFU (2LNH).
26554011 Nck1 contains the C-helix that competes with the C-helix in the VCA segment when WASP is in its autoinhibited state.
WASP and N-WASP proteins are required to initiate actin nucleation by activating actin-related protein (ARP)2/3 complex. WASP/N-WASP contains a GTPase-binding domain (GBD) at the N-terminus and a verprolin-homology, connector-helix, acidic motif (VCA) (also referred to as WCA as the V region is also called WH2) segment at the C-terminus. Under basal conditions the C-helix motif fits in the GBD domain closing the protein and preventing its nucleation promoting function (Kim,2000). Three factors participate in coordination to activate N-WASP in the membrane, a GTPase like CDC42 that binds the GBD domain, an acidic phospholipid like PtdIns(4,5)P2 and a SH3-domain-containing protein (like Nck) that binds to the PxxP motifs located between the GBD and the VCA segments (10360578; 11340081; 26554011). Nck can get a membrane localization by using its SH2 domain to bind to phosphorylated tyrosine-containing proteins like Nephrin that is a transmembranal protein. The co-localization of Nck and N-WASP allows the C-helix motif located in the linker space of the first and the second SH3 domains to bind to the GBD domain, out competing with the intramolecular C-helix in N-WASP. Additional bindings between N-WASP and Nck can occur due to interactions between the PxxP motifs in N-WASP and the second and third SH3 domains in Nck 26554011.

Interestingly, the effector proteins EspF and EspFU from the human pathogens Enterohaemorrhagic and Enteropathogenic Escherichia coli are able to activate WASP/N-WASP by using a mimic of the C-helix motif that is present in multiple copies, three in the case of EspF and between five and seven for EspFU (17893247; Cheng,2008; Sallee,2008). The motif is conserved in homologous proteins from Citrobacter rodentium, a mouse enteric bacterium. The actin polymerization activating potency is higher in the pathogenic proteins due to a multiple binding of the repeats, increasing the density of activated N-WASP molecules (Sallee,2008).
Position +1: Ile in WASP, WASL, NCK and EspF; Leu in WASP, NCK and EspF; Val in EspFU
Position +2: Val in WASP, WASL and NCK; Ala in EspF and EspFU
Position +3: Gly in WASP and WASL; Lys in NCK; Gln in EspF and EspFU
Position +4: Ala in WASP, WASL and EspF; Asn in NCK; Arg in EspFU
Position +5: Leu in all except in some fish (Iso)
Position +6: Met in WASP and WASL; Lys in NCK and EspF; Iso, Met and Val in any repeat in EspFU (7 Iso; 76 Met; 54 Val)
Position +7: Different in WASP and EspF; Glu in WASL; Asp in NCK; Gln in EspFU
Position +8: Val in WASP and WASL; Thr in NCK; His in EspFU
Position +9: Met in WASP and WASL; Leu in NCK, EspF and EspFU

A regular expression based on occurrence of instances would be the following:
[ILV][VA][^P][^P][LI][IMVK][^P][HTV][LM]
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LIG_CRIB_1 I[SG].P..{0,1}.[FA][EKRQ]H..[HT][VT][GSQ] 7493928 First described the Cdc42/Rac interactive binding motif.
9601050 Fragments as short as 75 to 94 of PAK1 still bound to either Cdc42 or Rac. Fragments 75-105 showed binding to Q61L Rac.GTP with Kd=1.9 µM.
9660763 They calculated that the 37 aas long region of WASP (221-257) still bound to Cdc42 with a Kd of 470 nM as measured by titration. Secondary structure was only observed for the longer fragment (W13).
9774440 and 10551809 showed that the substitution of His83 (position +9) and His86 (position +12) for Leu strongly decreased binding of PAK1 with Cdc42.
9774440 PAK1 75 to 132 (which includes the CRIB motif (75-88)) did not bind Cdc42.
22653441 The binding of PAK4 and Cdc42 was demonstrated by anti-tag coimmunoprecipitation.
22362774 The beta-strand is only 5 aas long ("EIIVL"). The correct alignment starts at Ile49 in SopB (Ile12 in PAK6). The Ile in position +1 (the only one conserved) was mutated in SopB and the (22362774) and the binding to Cdc42 got disrupted.
9528787 The Ile present in all Cdc42 binders at position +1 has been mutated for Asn and the affinity decreased 3-fold.
11940652 Ser at position +2 reduces interaction with CDC42. His at position +10 reduces interaction with CDC42.
12586692 His at position +10 reduces interaction with CDC42. His at position +12 reduces interaction with CDC42.
11940652 Mutations in the CRIB motif allows Cdc42-independent kinase activity and signaling ability, indicating the CRIB motif also works in the autoinhibition of Ste20.
10802735 They obtained the NMR structure of rat Pak1 and Cdc42 with overall very low wwPDB validation scores. In general, it does not overlap with any of the other structures of Rho GTPases, for example its RMS distance to Rac3 (2QME) is 3.16.
A linear motif of 14 to 15 residues long mediates the binding of different kinase and non-kinase proteins to the small Rho GTPases Cdc42 and Rac. The motif has been previously described as Cdc42 and Rac-interactive binding (CRIB) motif (7493928).

The p21-activated kinase (PAK) proteins are serine/threonine kinases activated by Cdc42 and Rac. They play roles in cytoskeleton dynamics, cell adhesion, apoptosis and mitosis. They link integrin activation with JNK MAP kinase pathway, phosphorylate and activate MEK1.

PAK orthologs have a well conserved N-terminal region. However, only the positions corresponding to the CRIB motif share conservation among paralogs.

Other unrelated proteins like the actin polymerization regulator WASP and the tyrosine-protein kinase PR2 are also binders of Cdc42 and Ras (9660763; 7493928).

In all these cases the presence of the CRIB motif is necessary for binding, but high affinity is only observed with additional molecular interactions that depend on an extended region C-terminal from the motif (9601050; 9660763).

Several crytallographic and NMR structures have been solved of the interaction of the CRIB motif and either Cdc42 or Rac (1EES; 1E0A; 2OV2; 2ODB; 1CEE; 4MIT; 4JSO; 1NF3; 4DID; 2QME), the comprehensive analysis of these structures show that around 26 amino acids are suficient to keep a static complex structure. The CRIB motif forms a beta aumentation with the small Rho-GTPase.
The bacterial protein SopB from Salmonella enterica binds to GDP-bound Cdc42 with a Kd=6uM +-2uM also creating a beta augmentation. However, the sequence is highly degenerated and is not covered by the current regular expression (22362774).
The putative paralog of PAK in Entamoeba histolytica binds to RacC from E. histolytica. The structure (4MIT) compared to PAK6 bound to Cdc42 (2ODB) shows that the helix present at the C terminal of the crystalized region is irrelevant for the interaction with the Rho GTPase.
first draft
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LIG_Vh1_VBS_1 ([IL][VILY].[^P]A[^P].[VIL][^P].[^P][VLMT][^P][^P][VL][VIL])|(DD[IL][VILY].[^P]A[^P].[VL][^P].[^P][VLM][^P]P[VL][VIL]) Izard,2004 Crystal structure of the VBS-N in Talin 1 with Vh1 from Vinculin.

22334306 The second alpha-helix in Talin 1 (VBS-C) binds to Vh1 in Vinculin.

Izard,2004 Talin 1 from Gallus gallus opens/activates human Vinculin.

Gingras,2006 Spot-peptide arrays to determine which positions that are or are not allowed in the binding VBS. Structures different helices in Talin in complex with Vh1 from Gallus gallus.

Gingras,2005 Crystal structure of Talin 1 from Gallus gallus with Vh1 from Gallus gallus.

Izard,2006 IpaA from Shigella flexneri contains two VBS motifs that bind in a mutually exclusive fashion to human Vinculin.

Hamiaux,2006 IpaA from Shigella flexneri contains two VBS motifs that bind simultaneously to two Vh1 domains from Vinculin.

Park,2011 VBS N and C terminal in sca4 from Rickettsia rickettsii.
Vinculin works as a linker that strengthens the association of Talin and F-Actin at sites of integrin activation allowing stronger actin binding and major stability of the sites of focal adhesion (23719537). Talin contains a small globular head and a long tail containing 63 predicted alpha helices. Apparently, some of these helices can form a tertiary structure when not activated, as shown by NMR experiments (Gingras,2006). After a substantial change in this tertiary structure, 11 out of the 63 helices are able to bind to Vh1 head domain of Vinculin, forming a helix bundle, as demonstrated by SPOT peptide analysis and crystallographic structures (Gingras,2006), the helical motif that allows the binding is referred as Vinculin Binding Site (VBS).

Interestingly, bacterial pathogens like Shigella flexneri and Rickettsia have developed mimic structures that resemble the architecture of the VBSs in Talin with the same biological function and co-localization with Talin that can induce actin polymerization without the need of integrin activation (Izard,2006; Hamiaux,2006; Park,2011).
The current regular expression matches some but not all the peptides that were confirmed as binders in a SPOT peptide analysis (Gingras,2005). In particular, it matches the one helix that has a crystal structure (1ZW2) demonstrating the binding but that it is unexpected to be a real one since it covers the binding site for the F-actin. A crystal structure (1ZVZ) showed that helix having a Met at the +1 position can bind Vh1 from Vinculin but after major changes in the side chains and the orientation of one alpha helix in Vh1. This Met in the +1 position was shown to impair the binding of VBS1 on a SPOT-peptide substitution array. Therefore, the current regular expression do not allows a Met in the +1 position.
Positions +4, +6, +9, +11 and +13 do not allow a Pro based on the SPOT-peptide substitution array. Position +14 allows a Pro when two Asp are present at position -2 and -1.
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MOD_ARK/PRK/AAK1_1 [LI]..Q.(T)G 12956961,
9885245,
11739778,
13679512,
Ricotta,2002
Optimal phosphorylation site motif for mammalian AAK1 and yeast PRK/ARK kinases that are involved in the regulation of endocytosis. A more relaxed version of the motif is [L/I/V/M]xx[Q/N/T/S]xTG first draft
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LIG_APP_AP2beta_1 [FL]..G[FL].DF Schmid,2006, 1E42
Motif binding to the side site of the C-terminal beta2-appendage domain of the large subunit beta2-adaptin. This interaction is part of the system for recruiting partners for assembly of clathrin-coated vesicles. first draft
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Lig_MHD_deltaCOP_1 W.{1,6}[WF] 26578768, 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 first draft
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LIG_MHD_FCHO_1 DPFxxxDPFxxDPF 27237791
25061211
The motif binds to mu humology domain (MHD) of FCHO with an affinity of 2μm. first draft
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MOD_LOK [KR]Y.[ST] 16616188 LOK kinase optimal phosphorylation site. LOK is a basophilic kinase with unusual Y preference at position 2. first draft
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eIF2alpha_binding_motif Rx[Gnl]x1-2Wxxx[Arlv]x[Dn][Rg]xRFxx[Rlvk][Ivc] 26100893
The eIF2α-binding motif is characterized by the consensus sequence Rx[Gnl]x1-2Wxxx[Arlv]x[Dn][Rg]xRFxx[Rlvk][Ivc], where capital letters are preferred and x is any residue. This eIF2α-binding motif is found in the PP1 regulatory subunits GADD34, CReP, and several viral proteins including, ICP34.5, DP71L, and CNPV231. first draft
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LIG_PEX19_mPTS_1 15133130 PEX19 is thought to be the receptor for importing peroxisomal membrane proteins by binding to a short mostly hydrophobic peptide, the mPTS. first draft
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LIG_AIR1_Trf4 IWRxY 21878619, 22402490, 3NYB The Air1-Trf4 interaction motif is important for TRAMP formation, which plays a major role in RNA surveillance and polyadenylation of RNA targets, marking them for exosomal degradation. The motif was found in yeast and presumably is conserved in an human orthologue of Air1. Motif in linker region between zinc knuckle 4 and 5 of Air1. first draft
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TRG_Transportin_M9nls_1 R..PY..P 7730395,
15703190,
16901787,
22778397,
16179349,
4FDD,
4JLQ,
2OT8,
2Z5K,
2Z5O,
2Z5N
Non-canonical NLS bound by transportin/karyopherin beta. Found in some RNA processing proteins, in T-box and ATF4/5 transcription factors. Always has a PY doublet, usually preceded by positively charged residues and also a weakly conserved second hydrophobic motif. Mutations in M9 class NLSes cause Di George syndrome (mutated in Tbx1) and ALS (mutated in FUS, EWS, TAF15). Observed instances are quite variable and likely require several motif patterns to capture the range of possibilities. first draft
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Lig_IntegrinA4B1_MLD MLD 14769041 Extracellular alpha4beta1, alpha9beta1 and alpha7beta4 Integrin-binding motif. Motif was first identified in snake venom disintegrins. Not sure if a native protein with MLD has been identified. first draft
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LIG_RGD_High RGDL..[LI] 25383667
4UM8
4UM9
Integrin alphaVbeta6 binds with high affinity to a RGDLXXL/I motif within the prodomains of ​TGF-β1 and ​TGF-β3. first draft
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LIG_MSL3 AFG..[LIV]..[LIMF].{4,10}F.LPW 21217699, 2Y0N Long extended peptide wrapping around the MRG domain of MSL3, with one part forming a short hairpin; highly conserved hydrophobic residues (mainly Phe) insert into different hydrophobic pockets on the MSL3 surface; found in MSL1 (subunit of the male-specific lethal complex involved in gene dosage compensation); (see also literature on WDR5-binding motifs in ELM). 21217699 discusses other proteins using similar surfaces/sequences for binding, see references therein; model presented here only describes core, should be extended at the N-terminus first draft
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LIG_MOF E.[LI].D[^P][^P][FY][^P][^P][^P]H[^P][KR] 21217699, 2Y0M Helical motif that binds the HAT domain of the histone acetyltransferase MOF; found in MSL1 (subunit of the male-specific lethal complex involved in gene dosage compensation) and NSL1 (subunit of the nonspecific lethal complex involved in transcription regulation and cell reprogramming) (see also literature on WDR5-binding motifs in ELM). first draft
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LIG_NRBOX_AR_2 F..LF 15178743 LBD-binding motif in the N-terminal region of androgen receptor that binds to coactivator-binding groove on androgen receptor (AR), competing with coactivators. This groove is deeper on AR compared to for instance estrogen receptor, which does not bind this motif. first draft
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LIG_Munc18/Sec1 D[RL].{3,4}[FL] 23572542,20884800,21139055,11879635,12426383,1MQS Conserved Munc18/Sec1-binding peptide present in N-terminal region of eukaryotic SNARE proteins, e.g. vertebrate syntaxin 5, yeast Sed5 and Ufe1, and arabidopsis SYP121. first draft
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LIG_KC1 F.RF 20884800,23572542 Motif in arabidopsis SNARE protein SYP121 required for binding to K+ channel subunit KC1; overlaps with a Sec1/Munc18-binding motif. first draft
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LIG_AP_GAE_2 W..[FW] 14973137,17506864,2DWX Motif in hinge region of GGA1, also in NECAP1 and amphiphysin II, that mediates interaction with the AP-1 gamma-ear domain; binds to same or overlapping site as LIG_AP_GAE_1 first draft
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LIG_OST ([FVL].C)|(C.[FVL]) 24685145,4M91,4M92 peptide that binds to the N33/Tusc3 (and maybe paralogous IAP/MagT1) subunit of the oligosaccharyl transferase (OST) complex to improve glycosylation efficiency; found in OST substrates; peptides can be accommodated in opposite orientations; peptide is covalently anchored to N33/Tusc3 via the cysteine residue (disulfide link); prefers Leu, Val or Phe in the -/+2 position relative to Cys; also backbone interactions first draft
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LIG_CagA 24474782, 4IRV N-terminal domain of the Cytotoxin Associated Gene A (CagA) of Helicobacter pylori binds to a 20aa long helical motif in the Apoptosis-stimulation protein p53-2 (ASPP2). first draft
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LIG_WIRS [FMYL].[TS]F.. 4N78
24439377
24439376
Motif binds to a conserved WAVE regulatory complex surface formed by Sra and Abi subunits. Motif therefore directly links diverse membrane proteins to the WRC and actin cytoskeleton first draft
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MOD_N-GLC_2 [DE].(N)[^P][ST].. 16619027
21209858
20523900
20847188
20581208
similar regular expression to MOD_N-GLC_1 but also found within bacteria and archea. bacterial N-glycosyltransferases exhibit a more stringent specificity for the acceptor site than the eukaryotic counterpart. This restricts glycosylation to a narrow set of polypeptides first draft
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CLV_MetAP1 ^M[ACGPS][^P]... Xiao,2010, 12665801, 18828628, 10574784, 16274222, 12475202 Target site for cleavage of N-terminal methionine by methionine aminopeptidase MetAP1. Overlapping substrate specificity with MetAP2 but MetAP1 cannot accommodate the larger side chains tolerated by MetAP2 (Thr and Val) in the P1' position due to its smaller active site. Disfavors acidic residues in positions P2' to P5'. His and Trp were underrepresented in P2' and P3' in the most active substrate peptides as determined by peptide library screening. Strong preference for Ala in P1'. first draft
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CLV_MetAP2 ^M[ACGPSTV][^P]... Xiao,2010, 12665801, 18828628, 10574784, 16274222, 12475202 Target site for cleavage of N-terminal methionine by methionine aminopeptidase MetAP2. Overlapping substrate specificity with MetAP1 but can accommodate larger side chains of Thr and Val in the P1' position due to its larger active site. Disfavors acidic residues in positions P2' to P5'. Disfavors Trp at P2' and P3'. first draft
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MOD_NatF ^(M)[LFIWK]... 21750686, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatF/NAA60. See 19660095 for nomenclature. Found only in higher eukaryotes, consequently MK termini are rarely found to be acetylated in yeast. first draft
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MOD_NatE ^(M)[KLMA]... 3TFY, 21900231, 21383206, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatE/NAA50. See 19660095 for nomenclature. Specificity partially overlaps with NatB and NatC. first draft
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MOD_NatD 19332560, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site in histones H2A and H4 for N-terminal acetylation (SGRGK termini) by NatD/NAA40 after cleavage of initiator methionine. See 19660095 for nomenclature. In vivo substrate specificity for NatD is determined by N-terminal 30-50 amino acid region in its histone substrates, instead of the first few residues (2-5) in case of the other N-acetyltransferases. first draft
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MOD_NatC ^(M)[LFIW]... 23613772, 10545125, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatC/NAA30. See 19660095 for nomenclature. Might also accept a Tyr residue in the second position. Specificity partially overlaps with NatB and NatE. first draft
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MOD_NatB ^(M)[DENQ]... 22814378, 12507466, 10545125, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for acetylation of N-terminal methionine by NatB/NAA20. See 19660095 for nomenclature. Specificity partially overlaps with NatC and NatE. first draft
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MOD_NatA ^([SATVCG])[^P]... 4KVM, 19420222, 10545125, 21383206, 23912279, 22405572, 21655309, 19660095, 20885971, 22718636, 19885390 Target site for N-terminal acetylation by NatA/NAA10 after cleavage of initiator methionine. See 19660095 for nomenclature. There might be subtle differences in specificity between yeast and human. NatA might also target N-terminal acidic residues, likely only in higher eukaryots and when acting independently from its auxiliary protein NAA15. first draft
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LIG_Talin [WY].{4}NP.Y 15362227, 20332112, 19903453, 19863457 Composite motif in the C-termal region of integrin. It is regulated by tyrosine phosphorylation and PTB domain binding at NPxY. Unphosphorylated form binds talin by beta addition. first draft
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LIG_FDF FDF|.DW 19285948, 2WAX, 2WAY, 23851565, 4BRU, 4BRW Motif in regulators of mRNA decapping like Pat1 and Edc3; mediates binding to the RecA2/Helicase_C (PF00271/IPR001650) domain of yeast Dhh1 and human Ddx6 RNA helicases. Edc3 contains the FDF variant, as well as yeast Pat1, while vertebrate Pat1 has the DW variant. Interactions mediated by this motif likely regulates binding of RNA to the helicase. In Edc3 the motif has been described as part of the FDF domain (PF09532/IPR025762), an alpha-helical domain with the conserved FDF sequence at the N-terminal. Structures show that additional binding elements determine the interactions. A helical acidic motif N-terminal to the FDF/DW motif in Pat1 binds to a second pocket on Dhh1, while a helical segment (F[DN]K) located C-terminal of the FDf motif in Edc3 binds yet another pocket on Ddx6/Dhh1. first draft
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FUN_FG_nucleoporin (FG)n 18688269, 12065398, 12372823, 17161424, 16338415 Motif present in nucleoporins that function as intramolecular cohesion elements imparting order to the FG domain and compacting its ensemble of structures into native premolten globular configurations. first draft
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LIG_Kln1_MELT_1 ..M[ED][LIVMF]T.. 24066227,
24361068,
4bl0
Repeated semi-conserved motifs with the consensus MELT are found in Kln1/Spc105 and bind to the BUB3 beta-propeller as part of the spindle assembly checkpoint. The motifs are phosphorylated on the Thr residue by Mps1. A structure of the motif in complex with the Bub3 domain has been solved in the yeast system. By sequence alignment, the mammalian MELT repeats might be longer than the yeast ones. The core MELT should be similar though. Backbone interactions extend beyond the core MELT motif: Pro might be excluded from some adjacent positions. first draft
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LIG_CYCLIN_2 L..P[ILVMF].[ILVMF] or LLPP 21945277, 21658602, Koivomagi,2013 These non-canonical cyclin boxes bind preferentially to the yeast cyclin Cln2 and enhance phosphorylation of Cdk substrates in a cyclin-specific manner. found in yeast. first draft
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Lig_CaM_1-5-10 ...[FILVW]...[FILVW]....[FILVW] Rhoads,1997 Several helical motif variants can bind calmodulin, including the Ca++ independent IQ motif and the 1-8-15 and the 1-5-10 motifs. The 1-5-10 motif is defined by the hydrophobic residue spacing. Other key features are lack of proline and a preference for positive and against negative charge. Additional info here

http://calcium.uhnres.utoronto.ca/ctdb/ctdb/

http://structbio.vanderbilt.edu/cabp_database/index.html
first draft
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Lig_CaM_1-8-15 [FILVW]......[FILVW].....[FILVW] Rhoads,1997 Several helical motif variants can bind calmodulin, including the Ca++ independent IQ motif and the 1-8-15 and the 1-5-10 motifs. The 1-8-15 motif is defined by the hydrophobic residue spacing. Other key features are lack of proline and a preference for positive and against negative charge. Additional info here

http://calcium.uhnres.utoronto.ca/ctdb/ctdb/

http://structbio.vanderbilt.edu/cabp_database/index.html
first draft
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LIG_Sliding_Clamp QL.L.[FL] 14729336 first draft
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LIG_SCF-TrCP1_2 [EDST][ESTD][GAS].{1,3}[STD] 19150432
14676825
15070733
15845771
18354483
17387146
18378670
15917222
15767683
Zhao,2010
20858893
23948254
non-canonical variants of the LIG_SCF-TrCP1_1 first draft
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LIG_Menin_MBM_2 20961854,
22327296
Bipartite interaction interface recognised by Menin. MBM1 (90nM) and MBM2 (1,400 nM) bind with different affinities but together bind with a much stronger affinity (6.8 nM). Exact residues are unknown but fall between residues 23-40. This entry may be fused with MBM_1 in light of the crystal structures of JunD and MLL1 complexes first draft
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LIG_Menin_MBM_1 ...R{0,2)FP[GA].P 20961854,
22327296,
3U85,
3U86
Part of Bipartite interaction interface recognised by Menin. MBM1 (90nM) and MBM2 (1,400 nM) bind with different affinities but together bind with a much stronger affinity (6.8 nM). MBM1 binds in an extended conformation. Crystal structures with MLL1 and JunD define this core part Positive charged residues c-terminally are also critical for the motif and if possible should be added to the core motif. first draft
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MOD_Citrullination ^M{0,1}[SGAT].R. 16567635
23818587
Peptidylarginine deiminase 4 (PAD4) is a Ca2+-dependent enzyme that converts arginine and methylarginine residues to citrulline. Originally identified in Histones, more recently PAD4-mediated citrullination of GSK3β has been discovered may not be only N-terminal first draft
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MOD_PKB_1 R.R[^PRK].[ST][FY^P] Yang,2002, 1O6L Improved P-site motif for PKB. Position -2 cannot allow Pro due to backbone H-bond. Position -2 considered not to allow R on structural grounds: this would differentiate relative to some other basophilic kinases. Position -2 has a strong T preference too. Position +1 is probably not strong enough to demand hydrophobic residue, though clearly favouring one. GSK3beta p-site is close to optimal. first draft
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Mod_PIMK_1 R.R[RKH^PDE].[ST][G^P] 16227208,2BZK PIM kinases of the CAMK-related group are mediators of cytokine signaling pathways in hematopoietic cells. Their P-sites are basophilic with a preference for R at the -5 and -3 positions like some other basophilic kinases. They have a weaker preference for positive charge at -2 (and cannot tolerate P). A weak G preference is found at +1 and P is rejected. first draft
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MOD_LRRK2_1 [FY].(T).R 21060682 The Parkinson's kinase LRRK2 phosphosite motif derived by oriented peptide library. Y is weaker than F at -3. K and R are generally favoured in the +1,+2,+3 positions of the motif. first draft
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LIG_Neur_NXXN N..N..L 19580805 N-rich motifs such as N..N..L in bearded and QN..NA in Delta reported to bind to the Neuralized E3 ligase. Motifs seem to play a role in both inhibition and activation of Notch signalling.

first draft
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LIG_PSI_ProlineMotif_1 P.PPP 15990112 Proline-rich sequence binding to small double alpha-helical module known as PSI A,B box or PFAM DUF1897 found as two or three copies in a few RNA-binding proteins e.g. PSI, KHRP. Aromatic residues on one helical face make hydrophobic interactions with Pro residues in the peptide motif which is found in U1-70k protein of the U1 snRNP. In fly, involved in P-element transposase alternative splicing. Strong phylogenetic conservation suggests that there is a more general cellular function. Not clear if this interaction is well enough described yet to make a motif pattern capturing the allowed Pro residue spacing and any possible additional residues. first draft
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TRG_NoDS RR[IL].{1,10}[ILVF][ILVF][ILVF] 22284675 Nucleolus targeting signals that results in sequestration of proteins by ncRNA first draft
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MOD_SUMO_SCM [PG].{0,4}[VILMAFP](K).E.{0,3}[PG] 10913186, 22829593, 12429819, 20150575 Synergy Control Motif (SCM) found in steroid receptors such as Androgen Receptor, Glucocorticoid Receptor transcription factors. SCM consists of a core 4 residue sumoylation site and within 3-4 residues N or C terminal of this site, a Pro or Gly residue is found. Mutations in these Pro or Gly residues are reported in various diseases including prostate and testicular cancer. first draft
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LIG_UBAN DF..ER 19185524, 18212736, 20428114 di-ubiquitin recognition motif found in ABIN proteins, Optineurin, and NEMO. The motif is required for inhibition of NFkB activation. Missense mutations disrupting the motif have been shown to be causal in diseases including Diffuse Large B-Cell Lymphoma and Amyothrophic Lateral Sclerosis. first draft
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LIG_JAK_Box1 P.[IV]P.P[EK] 12374810,
7896787
Box1 motif conserved in the common gamma subunit of cytokine receptors including erithropoietin receptor, interleukin3/5/6 receptors, prolactin receptor, interferon-gammaR receptor, and growth hormone receptors. The motif is required for association with JAK kinases. first draft
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LIG_sHSP_IxI_1 .I.[IV]. 23188086,
23340341
Oligomerisation motif of alpha-crystallins and related small heat shock proteins. first draft
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LIG_SH3_8 [RK]..[RK] 12176364
1H3H
Kojima,2004
non canonical SH3 binding motif confers specificity for the interaction between Gads and SLP-76 in T cell signaling.
12176364 analyses the binding using short peptides. SLP-76 contains two R..K motifs, but only the first (PSIDRSTK) binds, the second (TFPSRSTK) does not (or wasn't done)
first draft
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MOD_Spalmitoyl_3 (C)CIF 19092927 variant motif; instance does not match current RegEx instance in switches.elm: SWTI000549 CDC42_HUMAN (P60953-1) 188 191 first draft
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MOD_CDK_3 ([ST])P... Byeon,2005 variant motif; instance does not match current RegEx instance in switches.elm: SWTI000284 MK67I_HUMAN (Q9BYG3) 235 241 first draft
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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 first draft
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LIG_Dynein_DLC8_2 [KR].TMT 17029413;16981716 variant instance in switches.elm: SWTI000541
MYO5A_HUMAN (Q9Y4I1) 1286 1290
first draft
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CLV_CASPASE3_1 D..D 12637508 relaxed Caspase3-1 cleavage site instance in switches.elm: SWTI000550 CEAM1_MOUSE (P31809) 457 460 first draft
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LIG_S100A4_1 22460785,22483112,3ZWH,2LNK Ca2+ dependent binding of myosin IIA peptide to S100A4 dimer, involved in filament disassembly. The peptide binds across the S100A4 dimer surface (1:2 stoichiometry). Hydrophobic side chains insert into hydrophobic pockets on the dimer. In addition, charged and polar peptide residues form hydrogen bonds and salt bridges with complementary S100A4 residues. Composite binding site, will be added to switches.ELM. first draft
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LIG_S100A10_AnxA2_1 .[^FLVIMAWP][GLVAI][^FLVIMAWP][FIL][PVA][KHR][MIFLV][KHR].[GP][KR][FILV][^FLVIMAWP] 21949189, 23275167, 4DRW,4FTG Several regions in C-terminal of membrane-repair protein AHNAK bind to AnnexinA2-S100A10 (2:2) heterotetramer often localised at plasma membrane. A single AHNAK peptide binds across the tetramer surface, making contacts with all 4 components of the S100A10-AnxA2 complex. Binding mainly governed by hydrophobic interactions between AHNAK side chains and pockets on S100A10 (some with additional residues of AnxA2) and hydrogen bonds with backbone atoms of AHNAK. Composite binding site, will be added to switches.ELM. first draft
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TRG_NES Mazanka,2008 NES first draft
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LIG_BROMO_BET (K)[GILVMF]{0,1}[^MFYLW].(K) 2WP2
19794495
22464331
Diacetylation recgnition motif for bromodomain of BET family first BRDs of the BET family first draft
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LIG_BROMO 20502673,11080160 1E6I The Bromodomain binds acetylated lysine residues in the flexible N- and C-terminal tails of histones. first draft
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TRG_NLS Shin,2002 1594241 Duprez,1999 21092142 21182795 non-canonical nuclear localisation signals first draft
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MOD_EZH2 RKS 23063525 EZH2 can monomethylate the lysine on a RKS histone-like sequence on RORα leading to its subsequent ubiquitination through the chromo domain of DCAF1 see LIG_CHROMO for DCAF1 recognition motif first draft
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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. first draft
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LIG_MBT 20502673 1OYX 12842041 Malignant brain tumor (MBT) repeats have been implicated as methyl-lysine binding modules. first draft
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LIG_CHROMO ARK[ST] 20502673 1KNA 11859155 Chromo domains promote binding to methylated lysines in Histone H3 tails. first draft
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MOD_SUMO_PHOS [VILMAFP](K).[ST]. Picard,2012 Novel Sumoylation site found in Estrogen receptor beta connected to a GSK-beta phosphorylation site first draft
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LIG_KIX_CBP [DEST][LMYI]..[LIF][LIV] 22474372, 2KWF, 16253272, 2AGH, 9413984, 1KDX, 19220000, 17467953 hydrophobic motif found in transcription factors (FOXO3a, CREB, c-Myb, p53, TCF4...) that interacts with the KIX domain of CBP/p300 to recruit this transcription coactivator. Promiscuous as they might also bind to TAZ1 and TAZ2 domains of CBP/p300. For FOXO3a, phosphorylation of overlapping serine increases affinity. first draft
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LIG_MO25alpha_WEF_1 WEF 14730349, 19892943, 1UPK The WEF motif contributes to docking the STRADalpha pseudokinase to MOF25alpha in the LKB1-STRAD-MO25 complex System of increasing interest as LKB1 (STE11) is a tumour suppressor kinase and has recently been is associated with primary cilia and WNT/HH signalling
first draft
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LIG_SH2_IA (Y)[DE][DE][AFILVWY] 17956856 Subgroup IA, which consists of members of the SRC, SYK/ZAP-70, and TEC kinase families as well as the adaptor proteins NCK1 and NCK2, selects for the common motif (Y)[DE][DE][AFILVWY] first draft
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LIG_SH2_III (Y)..Q 17956856 Group III comprises the STAT family of SH2 domains.
first draft
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LIG_SH2_IID (Y)... 17956856 this is the generic motif for Group 2 SH2 domains. first draft
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LIG_SH2_IIC (Y)... 17956856 this is the generic motif for Group 2 SH2 domains. first draft
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LIG_SH2_IIB (Y)[ED].[AFILVWY] 17956856 Subgroup IIB selects for a hydrophobic residue at P+3 within the general consensus (Y)[ED].[AFILVWY]. The SHC and SHB families of adaptor proteins, BLNK, and SLNK all belong to this subgroup
first draft
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LIG_SH2_IIA (Y)[AFILVWY].[AFILVWY] 17956856 Subgroup IIA loosely selects for the degenerated motif (Y)[AFILVWY].[AFILVWY]. This subgroup is represented by the SH2 domains from several protein families that include VAV, phosphatidylinositol 3-kinase, PLCG1, PTPN, and SOCS.
first draft
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LIG_SH2_IE (Y)[DEKNPR][DEKNPR][AFILVWY] 17956856 this is the generic motif for Group 1 SH2 domains. first draft
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LIG_SH2_ID (Y)[DEKNPR][DEKNPR][AFILVWY] 17956856 this is the generic motif for Group 1 SH2 domains. first draft
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LIG_SH2_IC (Y).R 17956856 Subgroup IC,
identifiable by a strong proclivity for an Asn residue at P+2,
forms the second largest subgroup within group I with 18
members. It includes not only the GRB2/GRAP/GADS family
but also the GRB7/10/14 family, the tensin family, and the
Fes/Fer family.
first draft
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LIG_SH2_IB (Y)..[AFILVWY] 17956856 Subgroup IB, including SH2 domains from
SH2D1A, SHIP1/2, and CRK/CRKL, are
related to one another by a shared propensity for a hydropho-
bic residue at P+3. Selectivity at P+1 or P+2 for this group
of SH2 domains is wider than for subgroup IA
first draft
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TRG_AP2beta_CARGO_2 [FY]F.{6}W.[FY] 19287005 non-canonical AP2-beta2 binding found in isoform of PIPKIγ first draft
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TRG_NES_CRM1_2 L.{2,3}L.L 11074002 very general NES first draft
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LIG_PTB_Talin SPLH 1Y19, 2G35
12422219
Non-canonical PTB binding motif found to bind to the Talin PTB domain motif only found in PIP5K1C for far. Waiting for more instances before annotation first draft
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CLV_C14_Metacaspase 17028019,
18005666,
Sundstrom,2009,
21597462
Metacaspases are distantly related to caspases and are found in protozoa, fungi and plants. They are involved in regulation of different cell biological processes, like programmed cell death and development. Contrary to caspases which cleave specific after aspartate, metacaspases cleave specific after arginine and lysine. Depending on their prodomain metacaspases were distinguished into type I and II. Less is known about metacaspases' cleavage motif.
Only 3 metacaspases' substrates were described.

first draft
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TRG_LysEnd_APsAcLL_2 [DERQ].{2,4}L[LVI] 18315530
Kirchhausen,1999
Slight variation of TRG_LysEnd_APsAcLL_1 first draft
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TRG_MLS 22178138
10837244
16616497
The N-terminal Mitochondrial localisation signal recognised by Tom70. Could not define regular expression first draft
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LIG_IQ_3 [FILV]Q...[RK]G...[RK]..[FILVWYM] Rhoads,1997
8805510
8127365
12351846
Bahler,2002
extended IQ motif first draft
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LIG_IQ_2 [FILV]Q...[RK] Rhoads,1997
8805510
8127365
12351846
Bahler,2002
IQ-like motif. first draft
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LIG_PCNA_2 [ILVM][^ILVM][DHFM][ILVM] 11682605 slight variation on original PCNA motif first draft
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[Delete]
LIG_BIR_internal A.[AP]. 14523016 Internal BIR-binding site. In this case, precursor mitochondrial localisation signal is removed exposing BIR site first draft
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[Delete]
LIG_PI(4,5)P2 [KR].{3,4}K.[KR][KR] 9891784,Kojima,2004 lipid binding motif for PI(4,5)P2 first draft
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LIG_Filamin_2 Y..A[VIL]...[VIL] 16455489
2BRQ
Based on integrin binding to filamin
No mention of importance of threonines defined in LIG_Filamin
first draft
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LIG_TPR_4 [ST].[ST] 21454478
3Q4A
phosphorylated version of LIG_TPR found in Smad 1/5 first draft
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LIG_TPR_3 K[IL].{0,2}Q 18759457
17942943
internal TPR binding motif with similatities found in androgen receptor and vpu unsure of veracity first draft
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[Delete]
TRG_multiple 19482617 Review of several motifs responsible for internalization and trafficking
of cell-surface membrane receptors
NP.Y is mentioned in LIG_PTB_Phospho_1 first draft
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LIG_MIU [DE][LIVY].[LIV]A..[LIVY]..[DE]{DE] 16499958
2C7N
2C7M
19217402
MIU (motif interacting with ubiquitin; also known as IUIM or inverted UIM) first draft
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LIG_TAZ2 F.[DE]...L 10196247,19217391,16319895, 2KJE, 2K8F Binding motif for the TAZ2 domain in transcriptional adapter protein CBP/PCAF/p300 First attempt to annotate failed. Needs more information. A better structure for the P53 instance would be useful. first draft
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LIG_DUIM [DE].[LIVY]..A[LIVYM]A.S.[SA][DE] 16462748 2D3G double sided ubiquitin interacting motif first draft
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[Delete]
LIG_UIM [DE][DE]..[ILVY]..A[ILVY].S.. 16462748 12970172 1Q0V 2D3G 12750381 1O06 Ubiquitin interacting motif first draft
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MOD_N-GLC_3 NG. 20510933 21978957 Non-canonical N-glycosylations sites found in the mouse glycoproteome first draft
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MOD_N-GLC_4 N.V 20510933 21978957 Non-canonical N-glycosylations sites found in the mouse glycoproteome first draft
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LIG_PCNA_PIP_2 ...[LIM][DE].[FHY][FHY]. 19208623, 2ZVM,Kim,2010,Shibutani,2008 Non-canonical PIP box, missing the p1 glutamine. Mediates binding to PCNA. Found in Polη, Polκ. The PIP boxes of Xic1 in X. laevis and E2F in D. melanogaster overlap the PIP degron LIG_CRL4_Cdt2_1 and LIG_CRL4_Cdt2_2, respectively. first draft
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CLV_C14_Caspase-1 [WFYML][^P].D 1221285 1236692 15296730 Caspase-1 is involved in inflammation. Motif suggestion is based on in vitro data. Optimal described sequence is WEHD. For protein substrate see MEROPS or CutDB first draft
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LIG_WW_Nedd4L .(S)P.L(S)PN Aragon,2011, 2LAJ Motif in Smad3 that binds to the third WW domain of Nedd4L. Phosphorylation of Smad3 by CDK8/9 and GSK3 recruits ubiquitin ligase Nedd4-like via its third WW domain; second WW domain displaces Pin1 at WW motif upstream; leads to Smad3 destruction. first draft
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MOD_Geranyl_CAAXbox_1 (C).[LIVM][ILMV]$ 12702202 Motif modified by Geranylgeranyltransferase I (GGT1). Should replace current MOD_CAAXbox to define specificity. first draft
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MOD_Farnesyl_CAAXbox_1 (C).[LIVM].$ 12702202 Motif modified by Farnesyltransferase. Should replace current MOD_CAAXbox to define specificity. first draft
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[Delete]
LIG_DCUN1_1 (M)[IL].L Scott,2011 3TDZ Acetylated N-terminal methionine motif that mediates binding to the DCUN domain of E3 ligase DCN1 found in E2 ligase Ubc12. first draft
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LIG_LCK_1 C.CP 14500983 1Q69 1Q68 Found in CD4 and CD8. Beautiful mechanism where LCK contributes 2 cysteines and CD4/CD8 contribute 2 cysteines to bind zinc and form a "zinc clasp" binding site. 400nM affinity. Also buries a di-leucine sorting signal regulating trafficking. May not be a short linear motif by some definitions. first draft
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LIG_TKB (Y)[TS]..PT 20877636, 18273061, 3OB1, 3OB2 Recognition motif in EGFR and Sprouty2 for non-canonical SH2 domain (TKB domain) in E3 ubiquitin ligase c-Cbl first draft
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CLV_C14_Caspase4-5 [LIVMWYF][EDQ][^RKGL]D 1221285 1236692 Caspase-4 and -5 are involved in inflammation. Motif suggestion is based on in vitro data. Optimal described sequence is [WL]EHD. For protein substrate see MEROPS or CutDB first draft
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CLV_C14_Caspase-2 [DEIL].[DEFY]D 1221285 1236692 12920126 Caspase-2 induces the intrinsic apoptotic pathway during cell stress signaling. Motif suggestion is based on in vitro data. Optimal described sequence is DEHD. For protein substrate see MEROPS or CutDB first draft
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CLV_C14_Caspase-9 [^RK][EDQ]HD 1221285 1236692 11734640 Caspase-9 is an initiator caspase in the intrinsic apoptotic pathway and cleaves executor caspases. Motif suggestion is based on in vitro data. Optimal described sequence is LEHD. For protein substrate see MEROPS or CutDB first draft
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CLV_C14_Caspase-6 VLIT][EDQ][^DENQRKAPGS]D 1221285 1236692 19694615 21111746 Caspase-6 is an effector caspase during apoptosis. Putative role in Huntington’s and Alzheimer’s disease Motif suggestion is based on in vitro data. Optimal described sequence is VEHD For protein substrate see MEROPS or CutDB first draft
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LIG_TPR_2 [ILMV][DE]{1,2}[ILMV][DE]$ None Extension of the current over-defined TPR binding motif based on sequence analysis. first draft
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LIG_RIP_CTP SD[DE]DMGFGLFD$ 19073700 2JDL 11 residue long C terminal peptide motif of ribosomal stalk proteins which interact with ribosome inactivating proteins (RIP), which in turn leads to depurination of a specific Adenine residue of 28S rRNA and failure of the recruitment of elongation factors to the ribosomal GTPase-associated center, thus inhibition of the translation in the ribosome. first draft
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LIG_PUL_PLAA_1 [DE][DE][DE][DE]LY[AGS]$ 3EBB 19887378 Motif in ATPase VCP/p97 that binds to the PUL domain of PLAA. C-termianl motif with acidic extension that fits into a highly positive grove on the PUL domain surface. Involved in the regualtion of Ubiquitination. first draft
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LIG_Glycolytic_Aldolase W[DE]{2,3}W 3LGE 20129922 Motif that mediates binding to Aldolase A first draft
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LIG_SH3_9 SAMP 18786926 20509626 2RQU a non-canonical SH3 binding motif associated binding to ASAP1 and colocalized at microtubule ends. first draft
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LIG_Alpha-synuclein .DVF. 19762560 interaction with coiled coils of Synphilin-1 first draft
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LIG_Actin_DMD LK..E[ST] 9883911 actin binding motif found in the Dp71 dystrophin isoform first draft
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LIG_ECD_CRF LM..I$ 18801728, 3EHT Extracellular domain (ECD) of corticotropin-releasing factor (CRF) receptor 1 (CRFR1) binds to CRF via its C terminally amidated ligand motif. first draft
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LIG_BTB_SMRT [GL][IV][AT]T[IV]KE[AM]GRSIHEIPR 14690607, 1R2B Motif mediating binding of BCL6 BTB domain to SMRT first draft
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LIG_EAR 20935498 11487705 EAR motif mediates transcriptional repression of plant genes via recruitment of a histone deacetylase complex, which leads to chromatin modification. first draft
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TRG_Golgi 21283809 potential Golgi-retention motif and a number of conserved motifs with unknown function first draft
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LIG_SH3_7 [RK][RK].PXXPPXXP..[RK] 17437541 Motif in proline-rich domain of dynamin I that interacts with SH3 domain of endophilin I, consists of tandem core PxxP motif flanked by basic residues; bidirectional binding first draft
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LIG_SH3_6 [RK][RK].{9}[RK][RK].PXXPXX[RK]...[RK] 17437541 Motif in proline-rich domain of dynamin I that interacts with SH3 domain of syndapin I, consists of core PxxP motif flanked by basic residues; syndapin I binding sensitive to introduction of negative charges; bidirectional binding first draft
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MOD_acetyl_E2ligase_1 [KR]R[IL].KE 21791702 Motif found associated with the acetylation of ubiquitin E2 ligases first draft
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LIG_ARM [DEG].EGGGE.D...[FY]....L 20371349, 3L6Y Motif in JMD domain in C-terminal tail of cadherins that interacts with Armadillo repeats in p120 catenin first draft
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LIG_BH1_BH3 LA..GD 16475813 Motif of Bid-BH3 that binds to BH1 domain of Bcl-w. This interaction is lost upon Bcl-w lipid binding first draft
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LIG_Filamin ..(T)TT.. 20332112,Takala,2008, 2V7D Motif recognized by Filamin. First threonine must not be phosphorylated. Molecular switch. See LIG_Talin and LIG_14-3-3-3 (latter might need updating of regex as does not cover binding motif in integrins mentioned in 18550856) first draft
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LIG_Sin3_4 [FLW]..[ILV][ILV]... 21440557, 2L9S PAH motif in Pf1 (Q96QT6) binds to Sin3 (Q60520). Basically extends LIG_Sin3_3. (cave: pdb-structure features human motif but mouse sin3a) first draft
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LIG_TF2_FCP1_1 [DE]...[ILMV][AGS]..L..[DE][ILMF] 12732728,12591941, 1J2X Motif in carboxy terminus of FCP1 interacts with carboxy terminus of "Transcription initiation factor IIF subunit alpha" (RAP74). Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains. Might not be linear first draft
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LIG_CAVB_AID L.GY..WI 15141227, 1T0J Motif in Voltage-gated calcium channel beta-subunit (Cavb) binds to the conserved alpha-interaction domain (AID) of the same channel Interaction happens between subunits of calcium channel. Motif resides in structured region; found in multiple Voltage-dependent calcium channel subunits. first draft
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LIG_FERM_4 MDW.....[LI]F..[LF] 16615918,2YVC Motif that mediates binding to the FERM domain of Radixin found in NHERF-1. Binds different site to PSGL-1, NEP, CD44 and CD43. Nice mutational analysis in paper. first draft
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LIG_FERM_3 [KRQ]...Y..[ILV] 12554651,18076570,18753140, 2YVC, 2EMS, 2ZPY, 2EMT Motif that mediates binding to the FERM domain of Radixin found in PSGL-1, NEP, CD44 and CD43. Difficult consensus but all structures overlap the same binding site. first draft
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LIG_FERM_2 L...M..L..LM..L..IT 21642953,21321230, 3PZD Large cargo recognition helix in DCC, Ngn and Fz1A that binds to the FERM domain of Myosin-X. first draft
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LIG_20S [ILMV]Y.$ 21499243,20019667, 3IPM Binding site on the 20S protesome that is used by both assembly factors such as Pba1-Pba2 and activators such as PAN, Blm10 and PA28. first draft
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LIG_CORNRBOX_2 [IL]..[ILV][IL]..[ILVYF] Phelan,2010,3N00 An improved definition of the CoRNbox motif based on structural studies from SMRT and N-Cor. Should update current entry rather than make new entry as they are overlapping. first draft
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LIG_RCT L..L[KR].[KR] 21217703,3OWT Helical motif that mediates the binding to the RCT domain of yeast telomeric protein RAP1. Found in TAZ1(1.97uM) and Sir3(2.3uM) overlaps the binding site of a larger higher affinity disordered interface found in TRF2 (16.5nM). first draft
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LIG_Caveolin [WFY]....[WFY]..[WFY] 9325253 Motif mediating binding to Caveolin. Found in G-proteins, Src-like kinases, Ha-Ras, and eNOS. Also functions in a anti-parallel conformation. first draft
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MOD_phos_AURORA R.([ST]) 21712546,Alexander,2011 Canonical motif phosphorylated by Aurora kinase A/B first draft
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LIG_APH1 G...G 18061918, 21507970 conserved alpha helix binding motif; plays a role in maturation of the gamma-secretase complex, but may be involved in other recognitions (see ref2) earns a closer look (Mk) first draft
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LIG_AcetylCoA [QR]..G.[GA] 19660096 Conserved core motif responsible for acetyl coenzyme A binding as found in all members of the GNAT superfamily of N-acetyltransferases (GNAT, Pfam: PF00583 Acetyltransf_1) first draft
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MOD_HEME CP[ILMVFY] 7835342 Short sequence that has been shown to bind heme and is repeated up to 6 times. first draft
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DCK_dephos_PP1_4 F..[KR].[KR] 12115603,20376316 Docking motif for PP1 phosphatase found in several proteins involved in apoptosis such as Bcl-xL. first draft
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MOD_SPalmitoyl_X 15189153 Modification site by palmitoylation; may also mask other modifications or binding sites, e.g. by recognins extention of entries class 2 and class 4 first draft
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LIG_FERM_ICAM2 R...Y.V...W 12554651, 1J19 Cytosolic side motif in ICAM-2 binds to the PTB-like C domain of the FERM module. Important for membrane-associated cytoskeleton. Peptides with low similarity to ICAM-2 from other proteins also bind in this region of FERM so it may be difficult to define ELM motifs. first draft
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LIG_HBOX_DDB1 19966799 13aa structural motif, that must be located inside a disordered region, and which binds to DDB1. It's found in many DDB1 binding proteins but also in viral proteins, such as Hepatitis B virus protein X and parainfluenza virus 5 (formerly called simian virus 5 or SV5) protein V which use it to hijack DDB1. The problem is that it is not rigorously a sequence motif, rather many sequences can adopt this structural motif alpha-helix, but still, the author describes quite a few preferred positions. (Contact: D. Karlin) first draft
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LIG_cpSR43_ANK DPLG 18621669, 3DEP The DPLG motif binds L18p to cpSRP43. Part of a chloroplast system inserting light harvesting proteins into thylakoid membranes first draft
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LIG_Cdc20_Spo13 L.E...N 17493939 Degron in the yeast meiosis-specific protein SPO13 recognised by the cdc20 subunit of the APC. first draft
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MOD_SMAD (S)[IVLM](S)$ 9346908,18387785 C-terminal phosphorylation motif found in receptor-activated Smads. Phosphorylated by TGF-beta1 kinase after its activation first draft
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LIG_DHB_DAXX [DE]..[IL]..[WHFY][[WFHY] 21134643 Motifs in Rassf1C mediating binding to the DHB domain of the scaffold protein DAXX. Has structure but not yet in pdb (see paper). first draft
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LIG_N_degron_Doa10_Ac ^([MAVSTC]) 20110468 Acetylated N-terminal degron signal recognized by ubiquitin ligase Doa10. Promotes proteosomal degradation. first draft
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LIG_AGO_PIWI_1 WG 17891150 Mediates interaction with the Argonaute PIWI domain. Found in Argonaute-interacting protein Tas3. Difficult to annotate. Very variable other than conserved tryptophan. first draft
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LIG_BIR_Survivin ^AX(PT) 20705815 Most BIR domain interacting peptides are unmodified but the Survivin BIR domain recognises an N-terminal peptide with phosphothreonine in the third position. first draft
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LIG_TRADD YYD$ 9356494 Tumor necrosis factor receptor-associated death domain protein (TRADD) binding motif in LMP1 first draft
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TRG_VTS R.L.[EQ] 15591203,15591202 Vacuolar protein export signal. first draft
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LIG_PHDfingers_H3 ^...K 16728977 NURF and ING types of PHD finger bind histone H3 trimethylated lysine. first draft
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LIG_PKC [YF][SA][VI](Y)[QR].[YF]. 15851033 Phosphotyrosine motif in CDCP1 binding to the PKCd C2 domain. first draft
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TRG_Paranodin PGY 17093057 Paranodin trafficking repeat motif. first draft
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LIG_RHIM_1 [IV]Q[ILV]G 20346680 RIP homotypic interaction motif found in several programmed necrotic cell injury related proteins. Probably the core of a longer disordered interface first draft
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LIG_RNA_RGG RGG 8290338,12925994,12628254 Motif potentially involved in RNA binding in RGG transcriptional regulators. SMN Tudor domain binds dimethyl-Arg of RGG. first draft
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LIG_MIT_MIM2 [ILMV]P[DE]VP[ST]..LP 18606141, 2K3W VPS4 MIT domain binding "MIM2? motif found in a subset of ESCRT-III subunits first draft
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LIG_MYPT1 Y.Y Terrak,2004 Motif on PP1delta reciprocating the RV.F motif on the targeting subunit of MYPT1. MYPT1 also has an N-terminal helical motif interacting with PP1delta. first draft
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LIG_Notch DSL 17006545 Conserved N-terminal motif in Notch ligands. first draft
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Lig_PAH1_SID 16288918,18089292 Helical motif binding the PAH1 domain of the Sin3 corepressor. There are four PAH domains in Sin3 that are likely to bind helical peptides with different specificities. Reversed orientation binding has been observed for PAH1-binding helices. first draft
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LIG_PAS_STAT6 L..LL 14757047,12138096 Stat6 motif found in complex wit the PAS domain of NCoA, not the usual nuclear receptor. Indicates a more complex story. first draft
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LIG_R3IM [DE][DE][DE]EFE[DE] 18775730 Motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. first draft
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LIG_Sap1_Bbox F.L..L 11406578 SRF binding motif with beta-augmentation core. first draft
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MOD_acetylation 10656693,10607594,9744860,9774110,9809067 Acetylation targets in the nucleus beyond histone tails: p53, HMG I/Y, TCF, etc. first draft
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MOD_LammerK (RS)n 11827553,1577277,8772383 Many Lammer kinases (clk1-4, Doa, PK12) phosphorylate (RS)n motifs, regulating splicing. first draft
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MOD_MegPhos PPPSP 17555532 Necessary for phosphorylation of Megalin, possibly by GSK3. first draft
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MOD_methylation 8366133 Modification sites in histone tails and nucleolin. first draft
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MOD_Prk1p_1 [LVIM]....(T)G 13679512,11694597,19220811 Motif modified by Prk1p, a yeast kinase localised at cortical actin patches and regulating endocytosis. Substrates include epsins and the Bni1p formin. first draft
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TRG_chloroplast 10998602 Chloroplast transit peptides. first draft
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TRG_Dendritic LLY..[FYW] 16988049 Dendritic targeting motif. first draft
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TRG_ERM-PM RGGKYSV 17995939 Motif responsible for the recruitment of ERM proteins to the plasma membrane in neurogenesis. first draft
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TRG_Mit 11381593 Mitochondrial targetting peptides. first draft
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TRG_nucleolus 10469277,10050887,9731210 Nucleolar targeting signals. first draft
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TRG_Parasite_HT R.L.[EDQ] 18621946,19170882 Core motif for N terminal host-targeting (HT) motif composed of 11 amino acids that is found in Plasmodium and other parasites. first draft
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TRG_PEXEL_VTS 16046186 Export motif for RBC stage of the malaria parasite. Similar motif in potato blight. first draft
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TRG_RS (RS)n 12215544,1577277,8772383 C-terminal RS domain rich in arginine and serine residues (extensively phosphorylated) that promotes protein protein interactions and directs subcellular localization of SR splicing factors. first draft
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TRG_TGN YW 16978406 Retrograde endosome to trans-Golgi network motif. first draft
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LIG_TAZ1 LP.L / LPMSP 14594809,12778114,11959977, 1L8C, 1L3E Minimal region of a lager binding motif for the TAZ1 domain in transcriptional adapter protein CBP/PCAF/p300. Complicated binding read [19214187] for explanation. first draft
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TRG_TAT [ST]RR.FLK 16987314 Tat export consensus motif. first draft
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FAM_apoptotic XX...DD....D Motif found in apoptosis induction proteins: GPP synthases, Nox-a, Bad, Bid, Bik, yt-ppy-a, s81f. first draft
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CLV_GxGD G.GD 20021564 Motif that could be evolutionary conserved to allow cleavage of all possible gamma-secretase substrates. first draft
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LIG_CtBP_2 RRT..PPAL Nardini,2003 Another motif that binds to CtBP. first draft
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LIG_epitope MYPPPY 11418697 Epitope recognition motif present in CDC28 and conserved accross species. It is involved in the regulation of the immune response of T cells. first draft
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LIG_CKB_1 M.E.L.LC(ST)G.F 15707391,12545175 Triple phosphorylated docking motif in Claspin that binds checkpoint kinase CHK1 first draft
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LIG_Chromatin_H2A-H2B M.LRSG 18688256,16469929 Only 2 instances so far and the motif is completely conserved like this in both. Looking at the structures the SG (both small) is probably just there to allow the angles necessary for a hairpin Chromatin binding peptide, interacts with an acidic pocket formed by a H2A-H2B dimer. first draft
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FUN_GPIanchor 11814051,11677780,7482705 Glycosylphosphatidylinositol extracellular plasma membrane anchor. first draft
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LIG_COPII YNNSNPF, L..LE, D.E 12941276,15093828 Motifs involved in vesicle budding interactions of SNARES with COPII (subunits sec23/24). first draft
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LIG_MIT_MIM1 [DE]..L..RL..L[KR] 17928861, 2V6Y VPS4 MIT domain binding "MIM1? motif found in a subset of ESCRT-III subunits first draft
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LG_CyclophinA FGP.LP 15845542 Motif proposed to bind Cyclophin A. first draft
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LIG_clathr_ClatBox_Cter L[IVLMF].[IVLMF]$ 10449404 Variant clathrin box in yeast found at carboxy termini of e.g. some epsins. first draft
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LIG_CK1 F...F 15121840 Motif in NFAT and Per reported to dock CK1 kinase. Reminiscent of the FXXF motif in the PIF pocket kinases. first draft
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LIG_CH_Parvin_Backwards L..L[LM]..LE 18940607, 2VZD Motif mediating binding to the C-terminal calponin homology domain (CH(C)) of alpha-parvin. Possible molecular switch by binding the FAT domain targeting LD motifs of Paxillin. Can bind in an anti parallel orientation. first draft
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LIG_CH_Parvin_Forwards EL..L[LM]..L 18940607, 2VZD Motif mediating binding to the C-terminal calponin homology domain (CH(C)) of alpha-parvin. Possible molecular switch by binding the FAT domain targeting LD motifs of Paxillin. Can bind in an anti parallel orientation. first draft
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LIG_chromoshadow_EMSY [VILMF].[VILMF].[VILMF]..[VILMF] 16615912 Motif that binds to HP1 chromoshadow domains from EMSY. first draft
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LIG_Calnexin KPKKKKK 14988724 Poly Lysine motif found in Erp57 and responsible for Calnexin binding. Highly conserved in orthologs and always located at the C-terminal end. Might determine the specificity of Calnexin binding versus the protein disulfide-isomerase (PDI). first draft
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LIG_betaCatenin_armadillo 11136974,9774110 Motif responsible for the induced fit of 3-segmented IUP regions with the central KEGE-motif. K is not sampled but is acetylated by CBP to regulate the interaction. E/C-Cadherins have similar motif without K so not AC-regulated. Found in TCF/pangolin. first draft
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LIG_AP2alpha_3 W..[FW] 14565955 An AP-2 adaptor interaction motif initially identified in the long-splice isoform of Synaptojanin1. first draft
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LIG_AnkyrinG [VA]P[IL]A..E[SD]D 12716895,12829783 A conserved 9-amino acid motif required for ankyrinG binding. first draft
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LIG_alphaActin FGPVVA 1142354 Actin binding motif in plaque protein zyxin. Said to require alpha-actinin dimerisation. first draft
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LIG_integrin_extracell LDV 19255442 Another extracellular integrin binding motif. first draft
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FUN_Delta [DE].{2,4}NN[IL] 17006545 Motif conserved between invertebrates and vertebrates in Delta interacting proteins (Serrate/Jagged). Involved in the interaction with the E3 ubiquitin ligases Mib1 and Neur. first draft
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LIG_MDAS_MEF2 12700764 Motif found in the interaction between the MADS box of MEF2b and Cabin1. It aquires an amphipathic alpha-helix structure upon interaction. first draft
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LIG_Fn_binding LIPAD 19699715 Fibronectin binding motif on the C-terminus of the Leptospira adhesin LigB (LigBCtv), residues 1708-1712 containing sequence LIPAD with an beta-strand and nascent helical structure. first draft
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LIG_FF 12381297,16253993 Phosphorylated and possibly other motifs bind FF domains. Notably the RNA polII CTD. first draft
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LIG_IntA3B1 NVR 17034138 Integrin a3b1 binding motif in thrombospondin. first draft
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LIG_Hsc70 QLMLT 17978091,7649995 Motif in the Clathrin Heavy Chain Required for the Hsc70/Auxilin Uncoating Reaction. Sequence bound preferentially by the substrate groove of Hsc70 first draft
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LIG_FERM RSLE 17045809 A FERM domain binding motif in neurofascin. first draft
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LIG_Abox Littlepage,2002 Another destruction box proposed in Aurora A kinases. first draft
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FUN_UBX QA 16267091 Motif is present in Drosophila Ubx family of HOX genes and with pleiotropic functions in development. first draft
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FUN_Synaptotagmin KK...K 16987956 Motif required for efficient synaptic transmission. first draft
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FUN_Pin1_Isomerisation P[ST]P 12571275 Pin1 isomerization motif. first draft
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LIG_ERCC1 D[ST]G[AG]GF 17948053 Used by XPA to recruits ERCC1-XPF to nucleotide excision repair complexes first draft
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LIG_Integrin_Cell_Adhesion GRKRK 19617625 C-terminal motif of tropoelastin that can bind to cells in a divalent cation dependent manner. Might be an integrin binding motif required for cell adhesion. first draft
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FUN_Aurora 14752279 Double motif in TPX2 regulating Aurora kinase activity first draft
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LIG_integrin_TGFbeta DL..L 14572313 Integrin binding motif in TGFbeta. first draft
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LIG_LIM [IVLMF]I[IVLMF]R[IVLMF] 16616188 Motif that binds some LIM domains. It is part of larger conserved induced fit module where there might be a second LM02-LIM-binding motif. first draft
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Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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