Inhibitor of glycogen debranching 1
AF-A0A6C1DRY8-F1-v4
Share your feedback on structure with Google DeepMind Looks great Could be improved
Information
- 0
- 5
- 10
- 15
- 20
- 25
- 30
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-A7A255-F1 | Description Conserved protein Conserved protein | SpeciesSaccharomyces cerevisiae (strain YJM789) Saccharomyces cerevisiae (strain YJM789)... Saccharomyces cerevisiae (strain YJM789) | Sequence length 195 | Average pLDDT 59.5 |
AFDB accessionAF-A0A6C1DRY8-F1 | Description Inhibitor of glycogen debranching 1 Inhibitor of glycogen debranching 1 | SpeciesSaccharomyces pastorianus Saccharomyces pastorianus | Sequence length 195 | Average pLDDT 59.34 |
AFDB accessionAF-C8Z7V2-F1 | Description EC1118_1F14_1112p EC1118_1F14_1112p | SpeciesSaccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse)... Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) | Sequence length 195 | Average pLDDT 58.88 |
AFDB accessionAF-A0A0L8VRY4-F1 | Description IGD1p Cytoplasmic protein that inhibits Gdb1p glycogen debranching activity IGD1p Cytoplasmic protein that inhibits Gdb1p glycogen debranching activity ... IGD1p Cytoplasmic protein that inhibits Gdb1p glycogen debranching activity | SpeciesSaccharomyces boulardii (nom. inval.) Saccharomyces boulardii (nom. inval.)... Saccharomyces boulardii (nom. inval.) | Sequence length 195 | Average pLDDT 58.78 |
AFDB accessionAF-H0GFQ0-F1 | Description YFR017C-like protein YFR017C-like protein | SpeciesSaccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7) Saccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7)... Saccharomyces cerevisiae x Saccharomyces kudriavzevii (strain VIN7) | Sequence length 195 | Average pLDDT 58.66 |
AFDB accessionAF-A0A7I9EIP6-F1 | Description HN1_G0050290.mRNA.1.CDS.1 HN1_G0050290.mRNA.1.CDS.1 | SpeciesSaccharomyces cerevisiae Saccharomyces cerevisiae | Sequence length 195 | Average pLDDT 58.56 |
AFDB accessionAF-B3LUM6-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesSaccharomyces cerevisiae (strain RM11-1a) Saccharomyces cerevisiae (strain RM11-1a)... Saccharomyces cerevisiae (strain RM11-1a) | Sequence length 195 | Average pLDDT 58.5 |
AFDB accessionAF-A0A7I9ESQ0-F1 | Description SX2_G0050300.mRNA.1.CDS.1 SX2_G0050300.mRNA.1.CDS.1 | SpeciesSaccharomyces cerevisiae Saccharomyces cerevisiae | Sequence length 195 | Average pLDDT 58.44 |
AFDB accessionAF-A0A7I9EI24-F1 | Description EM14S01-3B_G0049640.mRNA.1.CDS.1 EM14S01-3B_G0049640.mRNA.1.CDS.1 | SpeciesSaccharomyces cerevisiae Saccharomyces cerevisiae | Sequence length 195 | Average pLDDT 58.31 |
AFDB accessionAF-A0A815YGM4-F1 | Description Igd1p Igd1p | SpeciesSaccharomyces cerevisiae PE-2 Saccharomyces cerevisiae PE-2 | Sequence length 195 | Average pLDDT 58.28 |
Visit our online training course
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
Data is available for academic and commercial use, under a CC-BY-4.0 licence.
EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice.
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.
Feedback and questions
If you want to share feedback on an AlphaFold structure prediction, consider using the feedback buttons at the top of each structure page. If you have any questions that are not covered in the FAQs, please contact alphafold@deepmind.com. If you have feedback on the website or experience any bugs please contact afdbhelp@ebi.ac.uk.
Let us know how the AlphaFold Protein Structure Database has been useful in your research at alphafold@deepmind.com.
Disclaimer
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.
Use of the AlphaFold Protein Structure Database is subject to EMBL-EBI Terms of Use.