Pentafunctional AROM polypeptide
AF-A4RD09-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-D1ZA70-F1 | Description Pentafunctional AROM polypeptide Pentafunctional AROM polypeptide | SpeciesSordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell)... Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) | Sequence length 1563 | Average pLDDT 91.42 |
AFDB accessionAF-B2B223-F1 | Description Pentafunctional AROM polypeptide Pentafunctional AROM polypeptide | SpeciesPodospora anserina (strain S / ATCC MYA-4624 / DSM 980 / FGSC 10383) Podospora anserina (strain S / ATCC MYA-4624 / DSM 980 / FGSC 10383)... Podospora anserina (strain S / ATCC MYA-4624 / DSM 980 / FGSC 10383) | Sequence length 1567 | Average pLDDT 91.21 |
AFDB accessionAF-Q6CJC4-F1 | Description Pentafunctional AROM polypeptide Pentafunctional AROM polypeptide | 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 1578 | Average pLDDT 90.61 |
AFDB accessionAF-B9WFG1-F1 | Description Pentafunctional AROM polypeptide Pentafunctional AROM polypeptide | SpeciesCandida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841)... Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) | Sequence length 1550 | Average pLDDT 90.51 |
AFDB accessionAF-B6QCA7-F1 | Description Pentafunctional AROM polypeptide 2 Pentafunctional AROM polypeptide 2 | SpeciesTalaromyces marneffei (strain ATCC 18224 / CBS 334.59 / QM 7333) Talaromyces marneffei (strain ATCC 18224 / CBS 334.59 / QM 7333)... Talaromyces marneffei (strain ATCC 18224 / CBS 334.59 / QM 7333) | Sequence length 1571 | Average pLDDT 90.39 |
AFDB accessionAF-C5DVG6-F1 | Description Pentafunctional AROM polypeptide Pentafunctional AROM polypeptide | 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 1589 | Average pLDDT 90.37 |
AFDB accessionAF-Q5AME2-F1 | Description Pentafunctional AROM polypeptide Pentafunctional AROM polypeptide | SpeciesCandida albicans (strain SC5314 / ATCC MYA-2876) Candida albicans (strain SC5314 / ATCC MYA-2876)... Candida albicans (strain SC5314 / ATCC MYA-2876) | Sequence length 1551 | Average pLDDT 90.33 |
AFDB accessionAF-A0A022VZT9-F1 | Description 3-phosphoshikimate 1-carboxyvinyltransferase 3-phosphoshikimate 1-carboxyvinyltransferase ... 3-phosphoshikimate 1-carboxyvinyltransferase | SpeciesTrichophyton rubrum CBS 288.86 Trichophyton rubrum CBS 288.86 | Sequence length 1277 | Average pLDDT 90.31 |
AFDB accessionAF-A0A022XQ62-F1 | Description 3-phosphoshikimate 1-carboxyvinyltransferase 3-phosphoshikimate 1-carboxyvinyltransferase ... 3-phosphoshikimate 1-carboxyvinyltransferase | SpeciesTrichophyton soudanense CBS 452.61 Trichophyton soudanense CBS 452.61 | Sequence length 1277 | Average pLDDT 90.31 |
AFDB accessionAF-A5H2P4-F1 | Description Pentafunctional AROM polypeptide 2 Pentafunctional AROM polypeptide 2 | SpeciesLodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239)... Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) | Sequence length 1551 | Average pLDDT 90.28 |
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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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