Yae1_N domain-containing protein
AF-G0WD70-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-C4QV68-F1 | Description Yae1_N domain-containing protein Yae1_N domain-containing protein | SpeciesKomagataella phaffii (strain GS115 / ATCC 20864) Komagataella phaffii (strain GS115 / ATCC 20864)... Komagataella phaffii (strain GS115 / ATCC 20864) | Sequence length 145 | Average pLDDT 86.88 |
AFDB accessionAF-I2GW52-F1 | Description Yae1_N domain-containing protein Yae1_N domain-containing protein | SpeciesTetrapisispora blattae (strain ATCC 34711 / CBS 6284 / DSM 70876 / NBRC 10599 / NRRL Y-10934 / UCD 77-7) Tetrapisispora blattae (strain ATCC 34711 / CBS 6284 / DSM 70876 / NBRC 10599 / NRRL Y-10934 / UCD 77-7)... Tetrapisispora blattae (strain ATCC 34711 / CBS 6284 / DSM 70876 / NBRC 10599 / NRRL Y-10934 / UCD 77-7) | Sequence length 170 | Average pLDDT 83.38 |
AFDB accessionAF-A0A1X7R233-F1 | Description Yae1_N domain-containing protein Yae1_N domain-containing protein | SpeciesKazachstania saulgeensis Kazachstania saulgeensis | Sequence length 163 | Average pLDDT 82.75 |
AFDB accessionAF-G0V591-F1 | Description Yae1_N domain-containing protein Yae1_N domain-containing protein | SpeciesNaumovozyma castellii (strain ATCC 76901 / BCRC 22586 / CBS 4309 / NBRC 1992 / NRRL Y-12630) Naumovozyma castellii (strain ATCC 76901 / BCRC 22586 / CBS 4309 / NBRC 1992 / NRRL Y-12630)... Naumovozyma castellii (strain ATCC 76901 / BCRC 22586 / CBS 4309 / NBRC 1992 / NRRL Y-12630) | Sequence length 163 | Average pLDDT 82.44 |
AFDB accessionAF-A0A7I9G2G4-F1 | Description EM14S01-3B_G0009690.mRNA.1.CDS.1 EM14S01-3B_G0009690.mRNA.1.CDS.1 | SpeciesSaccharomyces cerevisiae Saccharomyces cerevisiae | Sequence length 164 | Average pLDDT 82.19 |
AFDB accessionAF-Q6CUS4-F1 | Description KLLA0C02651p KLLA0C02651p | SpeciesKluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)... Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Sequence length 164 | Average pLDDT 82 |
AFDB accessionAF-A0A6C1DYS6-F1 | Description Ribosome biosynthesis protein lto1 Ribosome biosynthesis protein lto1 | SpeciesSaccharomyces pastorianus Saccharomyces pastorianus | Sequence length 162 | Average pLDDT 81.88 |
AFDB accessionAF-A0A816AXY0-F1 | Description Lto1p Lto1p | SpeciesSaccharomyces cerevisiae PE-2 Saccharomyces cerevisiae PE-2 | Sequence length 162 | Average pLDDT 81.88 |
AFDB accessionAF-A0A6V8S4X3-F1 | Description Protein LTO1 Protein LTO1 | SpeciesSaccharomyces cerevisiae Saccharomyces cerevisiae | Sequence length 162 | Average pLDDT 81.88 |
AFDB accessionAF-A0A1G4K5Z8-F1 | Description LAME_0G02520g1_1 LAME_0G02520g1_1 | SpeciesLachancea meyersii CBS 8951 Lachancea meyersii CBS 8951 | Sequence length 162 | Average pLDDT 81.69 |
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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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