DNA polymerase I, thermostable
AF-P19821-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.
PDB ID and chain | Description | Species | 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 | |
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Align in 3D | PDB ID and chain1tau_A_3 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 1 - 832P19821 | 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 96.2% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 3.00 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 | PDB ID and chain1bgx_T_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 1 - 832P19821 | 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 99.5% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.30 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 | PDB ID and chain4c8k_A_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 293 - 832P19821 | 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 100% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.17 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 | PDB ID and chain4n5s_A_3 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 281 - 832P19821 | 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 99.8% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.67 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 | PDB ID and chain3rtv_A_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 293 - 832P19821 | 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 100% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.90 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 | PDB ID and chain4elu_A_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 293 - 832P19821 | 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 100% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.80 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 | PDB ID and chain6fbc_A_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 293 - 832P19821 | 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 100% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.54 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 | PDB ID and chain3rrh_A_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 293 - 832P19821 | 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 100% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.80 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 | PDB ID and chain4elv_A_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 293 - 832P19821 | 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 100% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.90 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 | PDB ID and chain6fbe_A_1 | Description DNA polymerase I, thermostable DNA polymerase I, thermosta... DNA polymerase I, thermostable | Species Thermus aquaticus Thermus aquaticus | Residue range 293 - 832P19821 | 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 100% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.59 Resolution. Indicates the level of detail present in the 3D structure. Smaller value means finer details of the structure and higher quality. | |
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.
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-A0A6H1ZPQ0-F1 | Description Putative DNA polymerase Putative DNA polymerase | Speciesviral metagenome viral metagenome | Sequence length 838 | Average pLDDT 93.88 |
AFDB accessionAF-A0A6M3KTE6-F1 | Description Putative DNA polymerase Putative DNA polymerase | Speciesviral metagenome viral metagenome | Sequence length 838 | Average pLDDT 93.81 |
AFDB accessionAF-A0A6M3JAA0-F1 | Description Putative DNA polymerase Putative DNA polymerase | Speciesviral metagenome viral metagenome | Sequence length 838 | Average pLDDT 93.75 |
AFDB accessionAF-A0A6M3IN71-F1 | Description Putative DNA polymerase Putative DNA polymerase | Speciesviral metagenome viral metagenome | Sequence length 815 | Average pLDDT 93.5 |
AFDB accessionAF-A0A7V1PYP1-F1 | Description DNA polymerase I DNA polymerase I | SpeciesIgnavibacteria bacterium Ignavibacteria bacterium | Sequence length 771 | Average pLDDT 93.31 |
AFDB accessionAF-A0A6H1ZVQ7-F1 | Description Putative DNA polymerase Putative DNA polymerase | Speciesviral metagenome viral metagenome | Sequence length 824 | Average pLDDT 93 |
AFDB accessionAF-A0A3Q8ZMV4-F1 | Description POLAc domain-containing protein POLAc domain-containing protein | SpeciesMesorhizobium sp. M4B.F.Ca.ET.058.02.1.1 Mesorhizobium sp. M4B.F.Ca.ET.058.02.1.1... Mesorhizobium sp. M4B.F.Ca.ET.058.02.1.1 | Sequence length 916 | Average pLDDT 92.75 |
AFDB accessionAF-A0A6M3KG31-F1 | Description Putative DNA polymerase Putative DNA polymerase | Speciesviral metagenome viral metagenome | Sequence length 836 | Average pLDDT 92.75 |
AFDB accessionAF-A0A7S9E089-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesSalinimonas sp. G2-b Salinimonas sp. G2-b | Sequence length 859 | Average pLDDT 92.75 |
AFDB accessionAF-A0A2D5RMG6-F1 | Description DNA-directed DNA polymerase DNA-directed DNA polymerase | SpeciesEuryarchaeota archaeon Euryarchaeota archaeon | Sequence length 759 | Average pLDDT 92.69 |
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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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