ALY protein
AF-Q68VB6-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.
Start a structural similarity search to discover similar proteins.
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 |
---|---|---|---|---|
AFDB accessionAF-A0A835I1Y6-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesCoptis chinensis Coptis chinensis | Sequence length 248 | Average pLDDT 83.81 |
AFDB accessionAF-A0A1B7SK31-F1 | Description RRM domain-containing protein RRM domain-containing protein | SpeciesOgataea polymorpha Ogataea polymorpha | Sequence length 256 | Average pLDDT 80.06 |
AFDB accessionAF-C5DBQ5-F1 | Description KLTH0A04554p KLTH0A04554p | SpeciesLachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)... Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) | Sequence length 278 | Average pLDDT 78.69 |
AFDB accessionAF-A0A5J5AQ31-F1 | Description RRM domain-containing protein RRM domain-containing protein | SpeciesNyssa sinensis Nyssa sinensis | Sequence length 247 | Average pLDDT 77.88 |
AFDB accessionAF-A0A1G4M878-F1 | Description LAFE_0B04808g1_1 LAFE_0B04808g1_1 | SpeciesLachancea fermentati Lachancea fermentati | Sequence length 273 | Average pLDDT 77.62 |
AFDB accessionAF-A0A7I9E8M9-F1 | Description EM14S01-3B_G0052640.mRNA.1.CDS.1 EM14S01-3B_G0052640.mRNA.1.CDS.1 | SpeciesSaccharomyces cerevisiae Saccharomyces cerevisiae | Sequence length 300 | Average pLDDT 76.62 |
AFDB accessionAF-J8Q0Y2-F1 | Description Snp1p Snp1p | SpeciesSaccharomyces arboricola (strain H-6 / AS 2.3317 / CBS 10644) Saccharomyces arboricola (strain H-6 / AS 2.3317 / CBS 10644)... Saccharomyces arboricola (strain H-6 / AS 2.3317 / CBS 10644) | Sequence length 300 | Average pLDDT 76.38 |
AFDB accessionAF-A0A6C1EAU6-F1 | Description U1 snRNP component U1 snRNP component | SpeciesSaccharomyces pastorianus Saccharomyces pastorianus | Sequence length 302 | Average pLDDT 76.38 |
AFDB accessionAF-H0GWB0-F1 | Description Snp1p Snp1p | SpeciesSaccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7) Saccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7)... Saccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7) | Sequence length 300 | Average pLDDT 76.38 |
AFDB accessionAF-A0A0L8VNP1-F1 | Description SNP1p Component of U1 snRNP required for mRNA splicing via spliceosome SNP1p Component of U1 snRNP required for mRNA splicing via spliceosome ... SNP1p Component of U1 snRNP required for mRNA splicing via spliceosome | SpeciesSaccharomyces boulardii (nom. inval.) Saccharomyces boulardii (nom. inval.)... Saccharomyces boulardii (nom. inval.) | Sequence length 300 | Average pLDDT 76.25 |
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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.
Licence and attribution
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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).
AlphaFold Data Copyright (2022) DeepMind Technologies Limited.
AlphaMissense Copyright (2023) DeepMind Technologies Limited.
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The AlphaFold and AlphaMissense Data and other information provided on this site contain predictions with varying levels of confidence, is for theoretical modelling only and caution should be exercised in its use. It is provided 'as-is' without any warranty of any kind, whether expressed or implied. For clarity, no warranty is given that use of the information shall not infringe the rights of any third party. The information is not intended to be a substitute for professional medical advice, diagnosis, or treatment, and does not constitute medical or other professional advice. The AlphaFold and AlphaMissense Data have not been validated for, and are not approved for, any clinical use.
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