DUF3591 domain-containing protein
AF-A0A2C5ZA54-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-A0A1G4J9C5-F1 | Description LAFA_0E00980g1_1 LAFA_0E00980g1_1 | SpeciesLachancea sp. CBS 6924 Lachancea sp. CBS 6924 | Sequence length 1010 | Average pLDDT 69.06 |
AFDB accessionAF-C5DD95-F1 | Description KLTH0B09372p KLTH0B09372p | 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 1002 | Average pLDDT 68.81 |
AFDB accessionAF-A0A1G4ME84-F1 | Description LAFE_0E14312g1_1 LAFE_0E14312g1_1 | SpeciesLachancea fermentati Lachancea fermentati | Sequence length 1001 | Average pLDDT 68.75 |
AFDB accessionAF-A0A0C7MVR2-F1 | Description LALA0S10e00584g1_1 LALA0S10e00584g1_1 | SpeciesLachancea lanzarotensis Lachancea lanzarotensis | Sequence length 1010 | Average pLDDT 68.62 |
AFDB accessionAF-A0A109UZX7-F1 | Description HFR106Cp HFR106Cp | SpeciesEremothecium sinecaudum Eremothecium sinecaudum | Sequence length 1009 | Average pLDDT 68.56 |
AFDB accessionAF-Q751M7-F1 | Description AGL330Wp AGL330Wp | SpeciesAshbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)... Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) | Sequence length 1011 | Average pLDDT 68.56 |
AFDB accessionAF-C5DVJ5-F1 | Description ZYRO0D07216p ZYRO0D07216p | SpeciesZygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229) Zygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229)... Zygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229) | Sequence length 1003 | Average pLDDT 68.38 |
AFDB accessionAF-A0A1G4IRX3-F1 | Description LADA_0B01398g1_1 LADA_0B01398g1_1 | SpeciesLachancea dasiensis Lachancea dasiensis | Sequence length 1004 | Average pLDDT 68.25 |
AFDB accessionAF-A0A1S7HGV2-F1 | Description TAF1 (YGR274C) TAF1 (YGR274C) | SpeciesZygosaccharomyces parabailii Zygosaccharomyces parabailii | Sequence length 1001 | Average pLDDT 68.25 |
AFDB accessionAF-A0A1G4J9R8-F1 | Description LANO_0C08966g1_1 LANO_0C08966g1_1 | SpeciesLachancea nothofagi CBS 11611 Lachancea nothofagi CBS 11611 | Sequence length 1004 | Average pLDDT 68.25 |
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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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