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UPF0210 protein Mbur_0828

Reviewed
Reference proteome

AF-Q12XP4-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

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Information

Structure viewer
Model Confidence
pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test (lDDT-Cα). It is a measure of local accuracy - for interpreting larger scale features like relative domain positions see the “predicted aligned error” plot and corresponding tutorial. Confidence bands are used to colour-code the residues in the 3D viewer. The exact pLDDT value is shown when you mouseover the structure or the sequence. It can also be found in the B-factor fields of the downloadable coordinate files.

 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.

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SequenceNo structure available
Structure Tools
  • 6:12:01
    Mol* Plugin 4.5.0 [8/22/2024, 2:35:37 PM]
Model Confidence
pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test (lDDT-Cα). It is a measure of local accuracy - for interpreting larger scale features like relative domain positions see the “predicted aligned error” plot and corresponding tutorial. Confidence bands are used to colour-code the residues in the 3D viewer. The exact pLDDT value is shown when you mouseover the structure or the sequence. It can also be found in the B-factor fields of the downloadable coordinate files.
 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.
Scored residueAligned residue
01002003004000100200300400
  • 0
  • 5
  • 10
  • 15
  • 20
  • 25
  • 30
Expected position error (Ångströms)

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.

Similar structures Discover similar structures from the Protein Data Bank (PDB) and the AlphaFold Database clustered to 50% sequence identity (AFDB50) using Foldseek.
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Structure similarity clusterPredicted structures in the AlphaFold Protein Structure Database clustered using MMseqs2 and Foldseek. This data is provided by the AFDB Clusters.

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 DescriptionSpecies
Sequence length
Average pLDDT
AFDB accessionAF-A6UWW6-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein Maeo_1412
UPF0210 protein Maeo_1412
SpeciesMethanococcus aeolicus (strain ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3)

Methanococcus aeolicus (strain ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3)...

Methanococcus aeolicus (strain ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3)
Sequence length 458 Average pLDDT 94.88
AFDB accessionAF-A4FW97-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein MmarC5_0151
UPF0210 protein MmarC5_0151
SpeciesMethanococcus maripaludis (strain C5 / ATCC BAA-1333)

Methanococcus maripaludis (strain C5 / ATCC BAA-1333)...

Methanococcus maripaludis (strain C5 / ATCC BAA-1333)
Sequence length 458 Average pLDDT 94.81
AFDB accessionAF-Q466X7-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein Mbar_A3181
UPF0210 protein Mbar_A3181
SpeciesMethanosarcina barkeri (strain Fusaro / DSM 804)

Methanosarcina barkeri (strain Fusaro / DSM 804)...

Methanosarcina barkeri (strain Fusaro / DSM 804)
Sequence length 453 Average pLDDT 94.7
AFDB accessionAF-Q8Q0Q5-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein MM_0081
UPF0210 protein MM_0081
SpeciesMethanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)

Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)...

Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
Sequence length 453 Average pLDDT 94.69
AFDB accessionAF-Q6LXC5-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein MMP1427
UPF0210 protein MMP1427
SpeciesMethanococcus maripaludis (strain S2 / LL)

Methanococcus maripaludis (strain S2 / LL)...

Methanococcus maripaludis (strain S2 / LL)
Sequence length 458 Average pLDDT 94.67
AFDB accessionAF-A9A9N6-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein MmarC6_1246
UPF0210 protein MmarC6_1246
SpeciesMethanococcus maripaludis (strain C6 / ATCC BAA-1332)

Methanococcus maripaludis (strain C6 / ATCC BAA-1332)...

Methanococcus maripaludis (strain C6 / ATCC BAA-1332)
Sequence length 458 Average pLDDT 94.66
AFDB accessionAF-Q59059-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein MJ1665
UPF0210 protein MJ1665
SpeciesMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)...

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Sequence length 458 Average pLDDT 94.62
AFDB accessionAF-Q3ABZ3-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein CHY_1509
UPF0210 protein CHY_1509
SpeciesCarboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)

Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)...

Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)
Sequence length 452 Average pLDDT 94.6
AFDB accessionAF-B8CY23-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein Hore_14430
UPF0210 protein Hore_14430
SpeciesHalothermothrix orenii (strain H 168 / OCM 544 / DSM 9562)

Halothermothrix orenii (strain H 168 / OCM 544 / DSM 9562)...

Halothermothrix orenii (strain H 168 / OCM 544 / DSM 9562)
Sequence length 452 Average pLDDT 94.56
AFDB accessionAF-Q12XP4-F1
Reviewed (Swiss-Prot)
Reference proteome
Description UPF0210 protein Mbur_0828
UPF0210 protein Mbur_0828
SpeciesMethanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M)

Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M)...

Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M)
Sequence length 453 Average pLDDT 94.56
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Help

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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.

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:

  • We’re confident in the relative position of residue 200
  • We’re not confident in the relative position of residue 600

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.

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.

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).

 


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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