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LINE-1 retrotransposable element ORF2 protein

Reviewed
Reference proteome

AF-O00370-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

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Information

Structure viewer
 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
  • 21:45:20
    Mol* Plugin 4.5.0 [8/22/2024, 2:35:37 PM]
 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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Scored residueAligned residue
02004006008001k1.2k02004006008001k1.2k
  • 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.

AlphaMissense Pathogenicity Heatmap

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112751002003004005006007008009001,0001,1001,2005001000
1002003004005006007008009001,0001,1001,200GAVLISTCMDNEQRKHFYWPGAVLISTCMDNEQRKHFYWPAlternative amino acidsResidue sequence number
BenignUncertainPathogenic Reference
Amino acid present in the reference UniProt protein sequence, based on HG38
  • 0.0
  • 0.2
  • 0.3
  • 0.4
  • 0.5
  • 0.6
  • 0.7
  • 0.8
  • 1.0
  • -
Filter by category
0
0.34
0.00.34
0.34
0.56
0.340.564
0.56
1
0.5641
Similar structures Discover similar structures from the Protein Data Bank (PDB) and the AlphaFold Database clustered to 50% sequence identity (AFDB50) using Foldseek.
PDB ID
and chain
DescriptionSpecies Residue
range
E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
Seq.
identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
Res.
(Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
Align
in 3D
Align in 3D
PDB ID and
chain
8uw3_A_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1275O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
0.00e+0
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
98.3%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.20
Align in 3D
PDB ID and
chain
8c8j_A_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

238 - 1061O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
6.76e-85
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
85.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.10
Align in 3D
PDB ID and
chain
8sxt_A_3
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1275O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
5.08e-84
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
89.8%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.30
Align in 3D
PDB ID and
chain
8sxu_A_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1275O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
6.01e-81
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
89.8%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.66
Align in 3D
PDB ID and
chain
7n8k_A_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 238O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
3.71e-32
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
98.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.01
Align in 3D
PDB ID and
chain
8sp5_B_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 239O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
3.71e-32
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
98.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.23
Align in 3D
PDB ID and
chain
1vyb_A_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 238O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
4.20e-32
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
98.3%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.80
Align in 3D
PDB ID and
chain
1vyb_B_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 238O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
5.37e-32
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
98.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.80
Align in 3D
PDB ID and
chain
7n8k_B_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 238O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
9.96e-32
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
98.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.01
Align in 3D
PDB ID and
chain
8sp5_A_1
Description

LINE-1 retrotransposable element ORF2 protein

LINE-1 retrotransposable el...

LINE-1 retrotransposable element ORF2 protein
Species

Homo sapiens

Homo sapiens

Residue range

1 - 239O00370

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.22e-31
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
97.8%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.23
Items per page:
1 – 10 of 811
AF-O00370-F1
Current entry

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Aligned in 3D
Rotate and zoom structures in the 3D
viewer. Structures are aligned using alpha
carbon atoms as reference points. Once
aligned, RMSD values will appear in the
list below; lower values indicate greater
similarity between the two structures.
Toggle structures in both PDB and AFDB tables to view and align them with the entry structure in the 3D viewer. You can also download the aligned coordinates of the toggled structures and the entry structure.
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-A0A0G2KL83-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesDanio rerio
Danio rerio
Sequence length 1245 Average pLDDT 89.28
AFDB accessionAF-A0A3P9LHM7-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesOryzias latipes
Oryzias latipes
Sequence length 894 Average pLDDT 88.75
AFDB accessionAF-A0A671Y5T3-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesSparus aurata
Sparus aurata
Sequence length 1242 Average pLDDT 88.69
AFDB accessionAF-A0A669BJQ0-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesOreochromis niloticus
Oreochromis niloticus
Sequence length 1242 Average pLDDT 88.62
AFDB accessionAF-A0A3B3I0R1-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesOryzias latipes
Oryzias latipes
Sequence length 1241 Average pLDDT 88.44
AFDB accessionAF-A0A0G2KV08-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesDanio rerio
Danio rerio
Sequence length 1233 Average pLDDT 88.39
AFDB accessionAF-A0A3Q3BIJ9-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesKryptolebias marmoratus
Kryptolebias marmoratus
Sequence length 936 Average pLDDT 88.38
AFDB accessionAF-A0A3P9LWP5-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesOryzias latipes
Oryzias latipes
Sequence length 894 Average pLDDT 88.25
AFDB accessionAF-A0A0G2L6S5-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesDanio rerio
Danio rerio
Sequence length 1246 Average pLDDT 87.67
AFDB accessionAF-A0A3P8NYW9-F1
Unreviewed
Reference proteome
Description Reverse transcriptase domain-containing protein

Reverse transcriptase domain-containing protein ...

Reverse transcriptase domain-containing protein
SpeciesAstatotilapia calliptera
Astatotilapia calliptera
Sequence length 1205 Average pLDDT 87.62
Items per page:
1 – 10 of 1212

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).

AlphaFold Data Copyright (2022) DeepMind Technologies Limited.
AlphaMissense Copyright (2023) DeepMind Technologies Limited.

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The AlphaFold and AlphaMissense Data and other information provided on this site contain predictions with varying levels of confidence, is for theoretical modelling only and caution should be exercised in its use. It is provided 'as-is' without any warranty of any kind, whether expressed or implied. For clarity, no warranty is given that use of the information shall not infringe the rights of any third party. The information is not intended to be a substitute for professional medical advice, diagnosis, or treatment, and does not constitute medical or other professional advice. The AlphaFold and AlphaMissense Data have not been validated for, and are not approved for, any clinical use.

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