LiteFold/DisProt huggingface dataset:
Protein: DP02291 (UniProt P04486)
Region: residues 412	to 490
Annotation: molecular function activator activity (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492.
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r030
DisProt:DP01642r029
PDB:PDB:2PHE
PDB:PDB:2PHG
Protein: DP02291 (UniProt P04486)
Region: residues 469	to 485
Annotation: disorder (Structural state)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r014
Protein: DP02291 (UniProt P04486)
Region: residues 452	to 490
Annotation: disorder (Structural state)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r007
Protein: DP02291 (UniProt P04486)
Region: residues 475	to 484
Annotation: disorder to order (Structural transition)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r019
Protein: DP02291 (UniProt P04486)
Region: residues 469	to 485
Annotation: disorder to order (Structural transition)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r015
Protein: DP02291 (UniProt P04486)
Region: residues 452	to 490
Annotation: disorder to order (Structural transition)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r009
Protein: DP02291 (UniProt P04486)
Region: residues 469	to 485
Annotation: protein binding (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r016
Protein: DP02291 (UniProt P04486)
Region: residues 452	to 490
Annotation: protein binding (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r016
Protein: DP02291 (UniProt P04486)
Region: residues 475	to 484
Annotation: molecular function activator activity (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r018
Protein: DP02291 (UniProt P04486)
Region: residues 469	to 485
Annotation: molecular function activator activity (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r017
Protein: DP02291 (UniProt P04486)
Region: residues 452	to 490
Annotation: molecular function activator activity (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r010
Protein: DP02291 (UniProt P04486)
Region: residues 350	to 394
Annotation: disorder (Structural state)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r001
Protein: DP02291 (UniProt P04486)
Region: residues 403	to 490
Annotation: disorder (Structural state)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r002
Protein: DP02292 (UniProt Q96PU5)
Region: residues 400	to 480
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The α and β 13C chemical shifts analysis revealed that the segment connecting the WW2–WW3 pair (residues 400–480) lacks elements of a secondary structure in both the free and bound conformations, and is unaffected by binding of the Smad3 peptide.
Protein: DP02292 (UniProt Q96PU5)
Region: residues 400	to 480
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 80-amino-acid region connecting the WW2 and WW3 domains (dotted line) does not adopt a defined secondary or tertiary structure, as indicated by near-random 13C chemical shifts.
Protein: DP02294 (UniProt P63165)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 18 N-terminal amino acids for which electron densities are not observed in the SUMO-1–TDG crystal have been shown to be flexible in unconjugated SUMO-1 in solution
Cross-references: pdb:1wyw
Protein: DP02294 (UniProt P63165)
Region: residues 2	to 18
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SUMO-1 contains an N-terminal extension, which forms a flexible appendix that protrudes from the core protein
...However, only 34 NOEs could be used to characterize the flexible termini (Gly2 to Glu18 and Gln94 to Val101),
Cross-references: pdb:1a5r
Protein: DP02294 (UniProt P63165)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contained SUMO1(19–97)-AMSN, SAE1 amino acids (aa) 9–180 and 205–345, and UBA2 aa 5–217, 235–291, 305–548 and 608–640. As full-length proteins were used in crystallization, residues not observed in electron density were presumed disordered.
Cross-references: PDB:3KYC
Protein: DP02295 (UniProt Q05471)
Region: residues 599	to 627
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We observed that the Swr1 subunit uses the intrinsically disordered Swr1-Z domain to specifically recognize H2A.Z-H2B through interac- tions between the LxxLF motif of the Swr1-Z domain and the hydrophobic residues in the aC helix of H2A.Z. Mutation of
the hydrophobic residues in the LxxLF motif or deletion of the Swr1-Z domain leads to slow-cell-growth phenotype in the presence of caffeine.
Protein: DP02296 (UniProt P60761)
Region: residues 26	to 47
Annotation: disorder (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
Here, we report the structure of IQ peptides (24aa) of Nm/Ng complexed with CaM and their functional studies with full-length proteins. Nm/Ng and their respective IQ peptides are intrinsically unstructured; however, upon binding with CaM, IQ motifs adopt a helical conformation. Ser41 (Ser36) of Nm (Ng) is located in a negatively charged pocket in the apo CaM and, when phosphorylated, it will repel Nm/Ng from CaM.
Cross-references: PDB:4E50
Protein: DP02299 (UniProt P50498)
Region: residues 1	to 272
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The spectra for 3D7-6H under all conditions examined are remarkably similar, showing a single minimum at approximately 198 nm, indicative of a largely unstructured protein
Protein: DP02299 (UniProt P50498)
Region: residues 1	to 272
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
One-dimensional 1H NMR spectra of MSP2 under both physiological and acidic conditions show typical characteristics of an unstructured protein,
Protein: DP02299 (UniProt P50498)
Region: residues 1	to 270
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of both monomeric and polymeric 3D7 MSP2 are dominated by an ellipticity minimum at ~210 nm, indicating a high content of random coil
Protein: DP02299 (UniProt P50498)
Region: residues 1	to 272
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Furthermore, the axial ratio (a/b) of 17.2, calculated from the sedimentation coefficient and monomeric molecular mass assuming a prolate ellipsoidal shape (Table 1), indicates that the 3D7-6H monomer is significantly elongated in solution
Protein: DP02301 (UniProt Q71UI9)
Region: residues 39	to 48
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The H2A.Z.1 and H2A.Z.2 L1 loop regions are flexible.
Cross-references: PDB:3WAA
Protein: DP02301 (UniProt Q71UI9)
Region: residues 39	to 48
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 39-39 of H2A.V correlates with the canonical loop 1 of the H2A and H2B protein family.
([Pubmed ID: 23002134]: Furthermore, contacts between the H2A L1 loops of the two H2A–H2B dimers stabilize their association within the nucleosome)
Protein: DP02301 (UniProt Q71UI9)
Region: residues 39	to 48
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 39-39 of H2A.V correlates with the canonical loop 1 of the H2A and H2B protein family.
([Pubmed ID: 23002134]: Furthermore, contacts between the H2A L1 loops of the two H2A–H2B dimers stabilize their association within the nucleosome)
Protein: DP02302 (UniProt Q15843)
Region: residues 69	to 81
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The most striking difference between free (Whitby et al., 1998) and complexed NEDD8 is the C-terminal tail (Figure 5B), which rotates 30  about Leu69 to form the complex. Complex formation induces order in the C-terminal 3 residues, which are disordered in free NEDD8. The C-terminal tail adopts an extended strand-like conformation as it docks into the nucleotide binding pocket in UBA3.
Cross-references: PDB:1R4M
Protein: DP02302 (UniProt Q15843)
Region: residues 69	to 81
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal tail adopts an extended strand-like conformation as it docks into the nucleotide binding pocket in UBA3.
Protein: DP02302 (UniProt Q15843)
Region: residues 69	to 81
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal tail adopts an extended strand-like conformation as it docks into the nucleotide binding pocket in UBA3.
Protein: DP02309 (UniProt Q96RF0)
Region: residues 154	to 158
Annotation: protein binding (Molecular function)
Evidence: peptide array evidence used in manual assertion
Supporting statements:
The SNX18 WDDEW motif found to interact with LC3/GABARAP is a noncanonical motif because of the presence of the W and several acidic residues, and the lack of the hydrophobic residue in the L position.
Interestingly, this motif is also required for the SNX18 interaction with AP-1, an adaptor protein implicated in autophagosome biogenesis from the trans-Golgi network (Guo et al., 2012).
The interaction site was mapped to the SNX18 SH3-LC region (Fig. 7 A) and the exact sequence was determined by a peptide array covering the entire SNX18 SH3-LC sequence, where GST-GABARAP bound to all peptides containing 154-WDDEW-158 (Fig. 7 B), the same motif previously found to mediate binding of SNX18 to AP-1 (Håberg et al., 2008).
In summary, SNX18 interacts with Atg8 proteins through a WDDEW sequence in its SH3-LC region, and this interaction is required for localization of GFP-LC3 to SNX18-induced tubules and for GFP-LC3 spot formation.
The annotation includes the noncanonical motif WDDEW at position 154-158.
Protein: DP02309 (UniProt Q96RF0)
Region: residues 154	to 158
Annotation: protein binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The SNX18 WDDEW motif found to interact with LC3/GABARAP is a noncanonical motif because of the presence of the W and several acidic residues, and the lack of the hydrophobic residue in the L position.
Interestingly, this motif is also required for the SNX18 interaction with AP-1, an adaptor protein implicated in autophagosome biogenesis from the trans-Golgi network (Guo et al., 2012).
Mutation of one or both of the tryptophan residues (W154S and/or W158S) abolished the interaction with LC3/GABARAP (Fig. 7, C and D).
Furthermore, although tubules were still formed in cells expressing the myc-SNX18 W154S/W158S mutant, these were negative for GFP-LC3 (Fig. 7 E), and the number of GFP-LC3 spots was also significantly reduced compared with SNX18 WT (Fig. 7 F).
In summary, SNX18 interacts with Atg8 proteins through a WDDEW sequence in its SH3-LC region, and this interaction is required for localization of GFP-LC3 to SNX18-induced tubules and for GFP-LC3 spot formation.
Figure 7. A WDDEW sequence in the SNX18 LC region mediates the interaction with LC3/GABARAP. The annotation includes the noncanonical motif WDDEW at position 154-158. (C) Peptides with the sequence YGGYQASQGSDDDWDDEWDDSSTVADEPGAL (SNX18 WT) or with the first (SNX18 W154S), the second (SNX18 W158S), or both (SNX18 W154S/W158S) W mutated to S were spotted on membranes that were incubated with GST, GST-LC3B, or GST-GABARAP. Binding was analyzed as in B. (D) GFP-SNX18 WT and the indicated mutants were in vitro translated and incubated with GST-LC3B or -GABARAP, and their binding was analyzed as in A. (E) HeLa GFP-LC3 cells were transfected with myc-SNX18 W154S/W158S mutant, starved for 2 h, immunostained against myc, and analyzed by confocal imaging. Bar, 10 µm.
The annotation includes the noncanonical motif WDDEW at position 154-158.
Protein: DP02309 (UniProt Q96RF0)
Region: residues 154	to 158
Annotation: selective autophagy (Biological process)
Evidence: peptide array evidence used in manual assertion
Supporting statements:
The SNX18 WDDEW motif found to interact with LC3/GABARAP is a noncanonical motif because of the presence of the W and several acidic residues, and the lack of the hydrophobic residue in the L position. 


Interestingly, this motif is also required for the SNX18 interaction with AP-1, an adaptor protein implicated in autophagosome biogenesis from the trans-Golgi network (Guo et al., 2012).
The interaction site was mapped to the SNX18 SH3-LC region (Fig. 7 A) and the exact sequence was determined by a peptide array covering the entire SNX18 SH3-LC sequence, where GST-GABARAP bound to all peptides containing 154-WDDEW-158 (Fig. 7 B), the same motif previously found to mediate binding of SNX18 to AP-1 (Håberg et al., 2008).
 In summary, SNX18 interacts with Atg8 proteins through a WDDEW sequence in its SH3-LC region, and this interaction is required for localization of GFP-LC3 to SNX18-induced tubules and for GFP-LC3 spot formation.
The annotation includes the noncanonical motif WDDEW at position 154-158.
Protein: DP02309 (UniProt Q96RF0)
Region: residues 154	to 158
Annotation: selective autophagy (Biological process)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The SNX18 WDDEW motif found to interact with LC3/GABARAP is a noncanonical motif because of the presence of the W and several acidic residues, and the lack of the hydrophobic residue in the L position. 
Interestingly, this motif is also required for the SNX18 interaction with AP-1, an adaptor protein implicated in autophagosome biogenesis from the trans-Golgi network (Guo et al., 2012).
Mutation of one or both of the tryptophan residues (W154S and/or W158S) abolished the interaction with LC3/GABARAP (Fig. 7, C and D).
Furthermore, although tubules were still formed in cells expressing the myc-SNX18 W154S/W158S mutant, these were negative for GFP-LC3 (Fig. 7 E), and the number of GFP-LC3 spots was also significantly reduced compared with SNX18 WT (Fig. 7 F).
 In summary, SNX18 interacts with Atg8 proteins through a WDDEW sequence in its SH3-LC region, and this interaction is required for localization of GFP-LC3 to SNX18-induced tubules and for GFP-LC3 spot formation.
Figure 7. A WDDEW sequence in the SNX18 LC region mediates the interaction with LC3/GABARAP. The annotation includes the noncanonical motif WDDEW at position 154-158. (C) Peptides with the sequence YGGYQASQGSDDDWDDEWDDSSTVADEPGAL (SNX18 WT) or with the first (SNX18 W154S), the second (SNX18 W158S), or both (SNX18 W154S/W158S) W mutated to S were spotted on membranes that were incubated with GST, GST-LC3B, or GST-GABARAP. Binding was analyzed as in B. (D) GFP-SNX18 WT and the indicated mutants were in vitro translated and incubated with GST-LC3B or -GABARAP, and their binding was analyzed as in A. (E) HeLa GFP-LC3 cells were transfected with myc-SNX18 W154S/W158S mutant, starved for 2 h, immunostained against myc, and analyzed by confocal imaging. Bar, 10 µm.
The annotation includes the noncanonical motif WDDEW at position 154-158.
Protein: DP02309 (UniProt Q96RF0)
Region: residues 154	to 158
Annotation: protein binding (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Figure 7. A WDDEW sequence in the SNX18 LC region mediates the interaction with LC3/GABARAP. (A) GFP-p62 or -SNX18 full-length, SH3-LC, or PX-BAR regions were in vitro translated and incubated with GST-LC3B or -GABARAP. The resulting pulldowns were separated by SDS-PAGE. Bound proteins were detected by autoradiography and GST proteins by Coomassie blue staining.
The annotation includes the noncanonical motif WDDEW at position 154-158.
Protein: DP02309 (UniProt Q96RF0)
Region: residues 154	to 158
Annotation: protein binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Figure 7. A WDDEW sequence in the SNX18 LC region mediates the interaction with LC3/GABARAP. (B) 18-mer peptides covering the entire sequence of the SNX18 SH3-LC region were spotted on a membrane that was incubated with GST or GST-GABARAP, which were detected by immunoblotting against GST. The peptide sequences that specifically bound GST-GABARAP are shown with the common WDDEW motif in bold.
The annotation includes the noncanonical motif WDDEW at position 154-158.
Protein: DP02309 (UniProt Q96RF0)
Region: residues 59	to 224
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
The domain structure of SNX18 consists of an N‐terminal SH3 domain followed by an unstructured LC region and a C‐terminal PX‐BAR domain responsible for membrane binding and tubulation.
Protein: DP02311 (UniProt Q7DD77)
Region: residues 69	to 84
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Whereas MxiM requires the presence of a detergent ligand to form a folded structure, PilP has a folded domain, which requires no ligand for formation, but has significant portions of the structure in an unfolded state, particularly within the N terminus.
Cross-references: PDB:2IVW
Protein: DP02311 (UniProt Q7DD77)
Region: residues 20	to 69
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited digestion with chymotrypsin was found to yield a stable fragment; peptide sequencing was used to identify the N terminus, which starts from Glu69, and mass spectrometry demonstrated that the C terminus of the protein was not cleaved (data not shown).
Protein: DP02311 (UniProt Q7DD77)
Region: residues 164	to 181
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The C-terminus is unstructured even if it was not mentioned in the text.
Cross-references: PDB:2IVW