Kiwellin
AF-P85261-F1-v4
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Predicted aligned error (PAE)
Click and drag a box on the PAE viewer to select regions of the structure and highlight them on the 3D viewer.
PAE data is useful for assessing inter-domain accuracy – go to Help section below for more information.
PDB ID and chain | Description | Species | Residue range | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity Percentage of identical residues between aligned sequences over the aligned length. | Res. (Å) Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | Align in 3D | |
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Align in 3D | PDB ID and chain4x9u_A_1 | Description Kiwellin Kiwellin | Species Actinidia deliciosa Actinidia deliciosa | Residue range 25 - 213P84527 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 94.1% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.10 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain4pmk_A_1 | Description Kiwellin Kiwellin | Species Actinidia chinensis var. chinensis Actinidia chinensis var. ch... Actinidia chinensis var. chinensis | Residue range 25 - 213P85261 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 93.3% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.05 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain4x9u_B_1 | Description Kiwellin Kiwellin | Species Actinidia deliciosa Actinidia deliciosa | Residue range 25 - 213P84527 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 97.9% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.10 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain4pmk_B_1 | Description Kiwellin Kiwellin | Species Actinidia chinensis var. chinensis Actinidia chinensis var. ch... Actinidia chinensis var. chinensis | Residue range 25 - 213P85261 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 96.4% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.05 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain6fpg_E_2 | Description Kiwellin-1 Kiwellin-1 | Species Zea mays Zea mays | Residue range 33 - 198A0A1D6GNR3 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 57.1% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.80 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain6fpg_I_2 | Description Kiwellin-1 Kiwellin-1 | Species Zea mays Zea mays | Residue range 33 - 198A0A1D6GNR3 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 55.8% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.80 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain6fpg_H_2 | Description Kiwellin-1 Kiwellin-1 | Species Zea mays Zea mays | Residue range 33 - 198A0A1D6GNR3 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 55.8% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.80 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain6fpg_D_2 | Description Kiwellin-1 Kiwellin-1 | Species Zea mays Zea mays | Residue range 33 - 198A0A1D6GNR3 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 56.5% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.80 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain6ti2_A_2 | Description Ripening-related protein 3 Ripening-related protein 3 | Species Zea mays Zea mays | Residue range 1 - 193K7U7F7 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 59.2% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.75 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
Align in 3D | PDB ID and chain6ti2_E_2 | Description Ripening-related protein 3 Ripening-related protein 3 | Species Zea mays Zea mays | Residue range 1 - 193K7U7F7 | E-value Likelihood of a match between the query and target sequence in a structural alignment. The lower the E-value, the more significant the alignment. | Seq. identity 59.2% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.75 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
viewer. Structures are aligned using alpha
carbon atoms as reference points. Once
aligned, RMSD values will appear in the
list below; lower values indicate greater
similarity between the two structures.
AlphaFold database protein sequences clustered by the MMseqs2 algorithm (Steinegger M. and Soeding J., Nat. Commun. 9, 2018). Each cluster is comprised of sequences that fulfil two criteria: maintaining a maximum sequence identity of 50% and achieving a 90% bi-directional sequence overlap with the longest sequence of the cluster representative.
AFDB accession | Description | Species | Sequence length | Average pLDDT |
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AFDB accessionAF-N1QVM3-F1 | Description Putative ripening-related protein 4 Putative ripening-related protein 4 | SpeciesAegilops tauschii Aegilops tauschii | Sequence length 185 | Average pLDDT 89.75 |
AFDB accessionAF-A0A1F4ARZ5-F1 | Description Endolytic peptidoglycan transglycosylase RlpA Endolytic peptidoglycan transglycosylase RlpA ... Endolytic peptidoglycan transglycosylase RlpA | SpeciesBetaproteobacteria bacterium RIFCSPLOWO2_02_FULL_63_19 Betaproteobacteria bacterium RIFCSPLOWO2_02_FULL_63_19... Betaproteobacteria bacterium RIFCSPLOWO2_02_FULL_63_19 | Sequence length 200 | Average pLDDT 89.31 |
AFDB accessionAF-A0A446JUG2-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesTriticum turgidum subsp. durum Triticum turgidum subsp. durum | Sequence length 189 | Average pLDDT 88.5 |
AFDB accessionAF-A0A3B5YX31-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesTriticum aestivum Triticum aestivum | Sequence length 189 | Average pLDDT 88.5 |
AFDB accessionAF-A0A811MPN4-F1 | Description Hypothetical protein Hypothetical protein | SpeciesMiscanthus lutarioriparius Miscanthus lutarioriparius | Sequence length 189 | Average pLDDT 88.31 |
AFDB accessionAF-A0A7J9ENH4-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesGossypium trilobum Gossypium trilobum | Sequence length 179 | Average pLDDT 88.31 |
AFDB accessionAF-A0A3B5ZUM1-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesTriticum aestivum Triticum aestivum | Sequence length 190 | Average pLDDT 88.25 |
AFDB accessionAF-A0A811MV06-F1 | Description Hypothetical protein Hypothetical protein | SpeciesMiscanthus lutarioriparius Miscanthus lutarioriparius | Sequence length 189 | Average pLDDT 88.25 |
AFDB accessionAF-A0A446IVD0-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesTriticum turgidum subsp. durum Triticum turgidum subsp. durum | Sequence length 190 | Average pLDDT 88 |
AFDB accessionAF-A0A3B5XYI0-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesTriticum aestivum Triticum aestivum | Sequence length 190 | Average pLDDT 87.88 |
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How to interpret the Predicted Aligned Error
The Predicted Aligned Error (PAE) measures the confidence in the relative position of two residues within the predicted structure, providing insight into the reliability of relative position and orientations of different domains. Consider the human protein encoded by the gene GNE (Q9Y223). GNE has two distinct domains according to experimentally determined structures in the Protein Data Bank (PDBe-KB). Does AlphaFold confidently predict their relative positions? We can use the interactive Predicted Aligned Error (PAE) plot to answer this question. The PAE plot is not an inter-residue distance map or a contact map. Instead, the shade of green indicates the expected distance error in Ångströms (Å), ranging from 0 Å to an arbitrary cut-off of 31 Å. The colour at (x, y) corresponds to the expected distance error in the residue x’s position when the predicted and the true structures are aligned on residue y. The two low-error, dark green squares correspond to the two domains. By clicking and dragging, you can highlight these squares on the structure. If you want to remove the highlighting, click the cross icon. When selecting an off-diagonal region, the plot visually represents the relationship between the selected ranges on the sequence and structure. The x range corresponds to the selection for scored residues, highlighted in orange, while the y range of aligned residues is highlighted in emerald green. Let’s consider another inter-domain example, the human protein encoded by DIP2B (Q9P265). In this case, we have confidence in the relative position of scored residues around 1450 when aligned with residues around 850, suggesting a packing between the small central domains. Note that the PAE scores are asymmetrical, meaning there might be variations in PAE values between (x,y) and (y,x) positions. This is particularly relevant for loop regions with highly uncertain orientations, as seen on the DNA topoisomerase 3 (Q8T2T7).
A dark green tile corresponds to a good prediction (low error), whereas a light green tile indicates poor prediction (high error). For example, when aligning on residue 300:
The high PAE values across the whole inter-domain region indicate that for this particular protein, AlphaFold does not reliably predict the relative position of the domains.
Last updated
Last updated in AlphaFold DB version 2022-11-01, created with the AlphaFold Monomer v2.0 pipeline.
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If you make use of an AlphaFold prediction, please cite the following papers: Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).
Varadi, M et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Research (2024).
If you use data from AlphaMissense in your work, please cite the following paper: Cheng, J et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science (2023).
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AlphaMissense Copyright (2023) DeepMind Technologies Limited.
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