SMI1_KNR4 domain-containing protein
AF-A0A3M0W6V3-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-A0A1C1CQ98-F1 | Description Glucan synthesis regulatory protein Glucan synthesis regulatory protein | SpeciesCladophialophora carrionii Cladophialophora carrionii | Sequence length 528 | Average pLDDT 66.41 |
AFDB accessionAF-A0A2S4PUP7-F1 | Description SMI1_KNR4 domain-containing protein SMI1_KNR4 domain-containing protein | SpeciesErysiphe pulchra Erysiphe pulchra | Sequence length 489 | Average pLDDT 66.25 |
AFDB accessionAF-A0A072PYF2-F1 | Description SMI1_KNR4 domain-containing protein SMI1_KNR4 domain-containing protein | SpeciesExophiala aquamarina CBS 119918 Exophiala aquamarina CBS 119918 | Sequence length 451 | Average pLDDT 66.19 |
AFDB accessionAF-A0A0D2ENR0-F1 | Description Unplaced genomic scaffold supercont1.7, whole genome shotgun sequence Unplaced genomic scaffold supercont1.7, whole genome shotgun sequence ... Unplaced genomic scaffold supercont1.7, whole genome shotgun sequence | SpeciesFonsecaea pedrosoi CBS 271.37 Fonsecaea pedrosoi CBS 271.37 | Sequence length 549 | Average pLDDT 66.07 |
AFDB accessionAF-A0A7H9HNI4-F1 | Description SMI1_KNR4 domain-containing protein SMI1_KNR4 domain-containing protein | SpeciesTorulaspora sp. CBS 2947 Torulaspora sp. CBS 2947 | Sequence length 480 | Average pLDDT 65.88 |
AFDB accessionAF-A0A6A6BI75-F1 | Description SMI1_KNR4 domain-containing protein SMI1_KNR4 domain-containing protein | SpeciesAplosporella prunicola CBS 121167 Aplosporella prunicola CBS 121167 | Sequence length 501 | Average pLDDT 65.69 |
AFDB accessionAF-C6HG70-F1 | Description 1,3-beta-glucan biosynthesis protein 1,3-beta-glucan biosynthesis protein ... 1,3-beta-glucan biosynthesis protein | SpeciesAjellomyces capsulatus (strain H143) Ajellomyces capsulatus (strain H143)... Ajellomyces capsulatus (strain H143) | Sequence length 490 | Average pLDDT 65.62 |
AFDB accessionAF-A0A6A6DQ89-F1 | Description Cell wall assembly and cell proliferation coordinating protein Cell wall assembly and cell proliferation coordinating protein ... Cell wall assembly and cell proliferation coordinating protein | SpeciesZopfia rhizophila CBS 207.26 Zopfia rhizophila CBS 207.26 | Sequence length 512 | Average pLDDT 65.44 |
AFDB accessionAF-A0A0B1P532-F1 | Description Putative glucan synthesis regulatory protein Putative glucan synthesis regulatory protein ... Putative glucan synthesis regulatory protein | SpeciesUncinula necator Uncinula necator | Sequence length 499 | Average pLDDT 65.44 |
AFDB accessionAF-A0A178AXB9-F1 | Description Cell wall assembly and cell proliferation coordinating protein Cell wall assembly and cell proliferation coordinating protein ... Cell wall assembly and cell proliferation coordinating protein | SpeciesStagonospora sp. SRC1lsM3a Stagonospora sp. SRC1lsM3a | Sequence length 528 | Average pLDDT 65.31 |
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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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Disclaimer
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