Protein STE5
AF-P32917-F1-v4
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Mol* 3D Viewer
TED Domains and Predicted Aligned Error (PAE)

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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 |
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AFDB accessionAF-Q6BLG1-F1 | Description DEHA2F13728p DEHA2F13728p | SpeciesDebaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968)... Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) | Sequence length 910 | Average pLDDT 72.75 |
AFDB accessionAF-H8XBF6-F1 | Description Far1 protein Far1 protein | SpeciesCandida orthopsilosis (strain 90-125) Candida orthopsilosis (strain 90-125)... Candida orthopsilosis (strain 90-125) | Sequence length 906 | Average pLDDT 67.44 |
AFDB accessionAF-W0TBY0-F1 | Description Cyclin-dependent kinase inhibitor FAR1 Cyclin-dependent kinase inhibitor FAR1 ... Cyclin-dependent kinase inhibitor FAR1 | SpeciesKluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275) Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275)... Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275) | Sequence length 921 | Average pLDDT 66.25 |
AFDB accessionAF-A0A0A8L042-F1 | Description WGS project CCBQ000000000 data, contig 00041 WGS project CCBQ000000000 data, contig 00041 ... WGS project CCBQ000000000 data, contig 00041 | SpeciesKluyveromyces dobzhanskii CBS 2104 Kluyveromyces dobzhanskii CBS 2104 | Sequence length 887 | Average pLDDT 65.19 |
AFDB accessionAF-A0A5P2UA18-F1 | Description Far1 Far1 | SpeciesKluyveromyces lactis Kluyveromyces lactis | Sequence length 878 | Average pLDDT 64.69 |
AFDB accessionAF-A0A7G3ZEV2-F1 | Description RING-type domain-containing protein RING-type domain-containing protein | SpeciesTorulaspora globosa Torulaspora globosa | Sequence length 925 | Average pLDDT 61.38 |
AFDB accessionAF-A0A0P1KR13-F1 | Description LAQU0S06e00518g1_1 LAQU0S06e00518g1_1 | SpeciesLachancea quebecensis Lachancea quebecensis | Sequence length 956 | Average pLDDT 60.5 |
AFDB accessionAF-C5DSP8-F1 | Description ZYRO0C02002p ZYRO0C02002p | 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 881 | Average pLDDT 60.31 |
AFDB accessionAF-A0A1G4K8H8-F1 | Description LAME_0G09164g1_1 LAME_0G09164g1_1 | SpeciesLachancea meyersii CBS 8951 Lachancea meyersii CBS 8951 | Sequence length 965 | Average pLDDT 60.19 |
AFDB accessionAF-A0A4C2E720-F1 | Description RING-type domain-containing protein RING-type domain-containing protein | SpeciesZygosaccharomyces mellis Zygosaccharomyces mellis | Sequence length 883 | Average pLDDT 59.25 |
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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.
How to use The Encyclopedia of Domains
The Encyclopedia of Domains (TED) is a comprehensive resource that identifies and classifies protein domains within the AlphaFold Database using deep learning-based domain parsing and structure comparison. TED domains that share significant structural similarity with a previously characterised CATH domain are labelled with their predicted classification at the Topology/Fold level (3-level C.A.T. identifier) or Homologous Superfamily level (4-level C.A.T.H. identifier). Domains without classification labels indicate no similarity to CATH domains used during TED’s classification workflow. You can visualise TED Domains in the AlphaFold database entries in both the Mol* 3D Viewer and the domain annotation track displayed above the interactive PAE plot. Hovering and clicking on an individual domain track opens a tooltip with details such as the total number of residues (length), its position within the protein sequence (boundaries), the average pLDDT score, the 3-level C.A.T or 4-level C.A.T.H classification identifier and a quality metric for the domain assignment. Learn more in our FAQ. Let’s explore some examples: Hemoglobin subunit gamma-1 (AF-P69891-F1). This protein’s PAE shows high confidence in the relative positions of almost all residues. TED identifies one domain, spanning residues 5 to 142, with a superfamily assignment. Note that the Domain annotation track and the Mol* 3D Viewer structure colourings are mapped to individual domain boundaries and not classification levels. Therefore, an entry with multiple domains of the same Fold or Homologous Superfamily will show different colours for each domain. For example, the Bacterial Ig-like domain family protein (AF-A0A009R2D9-F1) contains twelve domains of varying quality, mostly assigned to the same Homologous Superfamily, but each domain has a distinct colour. Other important examples to better understand the complexity of protein architectures: SPR protein (AF-A0A836E5A2-F1), this entry contains one domain with insertions between segments, resulting in three boundaries, according to TED data. This illustrates how a single domain can have discontinuous segments in the sequence. Inosine-5'-monophosphate dehydrogenase (AF-Q21KQ8-F1) here, where a split domain (Domain 1, green) has another domain (Domain 2, orange) nested between its segments. This demonstrates the complexity of domain architectures compared to sequence. In the help section How to interpret the Predicted Aligned Error, we discussed the multi-domain protein like Disco-interacting protein 2 homolog B (AF-Q9P265-F1). With the integration of TED data, we see that the PAE shows a high confidence in the relative positions of domain 5 and domain 3. In the DUF5621 domain-containing protein (AF-Q5ZSU4-F1), TED identifies distinct domains, and the PAE shows an overall high confidence in the relative position of all domains. Some entries might not contain TED domains, such as the TrpR gene coding for the trp operon repressor protein (AF-A0A376RRE1-F1). There are several reasons why an entry might not have any TED domains, including the structural element does not qualify as a distinct domain according to TED's criteria, the fragment might not contain a complete domain or the overall entry has a very low pLDDT.
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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