Tyrosine recombinase XerA
AF-Q8TZV9-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 chain5hxy_D_1 | Description Tyrosine recombinase XerA Tyrosine recombinase XerA | Species Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) Thermoplasma acidophilum (s... Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) | Residue range 1 - 283Q9HIM5 | 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 38.2% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.50 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 chain5hxy_A_1 | Description Tyrosine recombinase XerA Tyrosine recombinase XerA | Species Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) Thermoplasma acidophilum (s... Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) | Residue range 1 - 283Q9HIM5 | 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 37.8% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.50 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 chain5hxy_E_1 | Description Tyrosine recombinase XerA Tyrosine recombinase XerA | Species Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) Thermoplasma acidophilum (s... Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) | Residue range 1 - 283Q9HIM5 | 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 38% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.50 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 chain5hxy_C_1 | Description Tyrosine recombinase XerA Tyrosine recombinase XerA | Species Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) Thermoplasma acidophilum (s... Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) | Residue range 1 - 283Q9HIM5 | 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 37.1% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.50 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 chain5hxy_B_1 | Description Tyrosine recombinase XerA Tyrosine recombinase XerA | Species Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) Thermoplasma acidophilum (s... Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) | Residue range 1 - 283Q9HIM5 | 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 36.8% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.50 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 chain5hxy_F_1 | Description Tyrosine recombinase XerA Tyrosine recombinase XerA | Species Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) Thermoplasma acidophilum (s... Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) | Residue range 1 - 283Q9HIM5 | 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 38.4% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.50 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 chain2a3v_A_3 | Description Integron integrase IntIA Integron integrase IntIA | Species Vibrio cholerae Vibrio cholerae | Residue range 1 - 320O68847 | 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 26.3% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.80 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 chain2a3v_C_3 | Description Integron integrase IntIA Integron integrase IntIA | Species Vibrio cholerae Vibrio cholerae | Residue range 1 - 320O68847 | 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 26.7% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.80 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 chain2a3v_B_3 | Description Integron integrase IntIA Integron integrase IntIA | Species Vibrio cholerae Vibrio cholerae | Residue range 1 - 320O68847 | 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 26.5% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.80 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 chain6en2_A_1 | Description Int protein Int protein | Species Enterococcus faecalis Enterococcus faecalis | Residue range 82 - 397Q7BP35 | 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 21.3% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.67 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-A0A2N5FV06-F1 | Description Recombinase Recombinase | SpeciesBacillus sp. UMB0728 Bacillus sp. UMB0728 | Sequence length 334 | Average pLDDT 94.56 |
AFDB accessionAF-A0A0H4KGH3-F1 | Description Recombinase Recombinase | SpeciesPriestia filamentosa Priestia filamentosa | Sequence length 334 | Average pLDDT 94.56 |
AFDB accessionAF-G4EV66-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesBacillus subtilis subsp. subtilis str. SC-8 Bacillus subtilis subsp. subtilis str. SC-8... Bacillus subtilis subsp. subtilis str. SC-8 | Sequence length 333 | Average pLDDT 94.5 |
AFDB accessionAF-A0A142Y8S7-F1 | Description Site-specific tyrosine recombinase XerD Site-specific tyrosine recombinase XerD ... Site-specific tyrosine recombinase XerD | SpeciesPirellula sp. SH-Sr6A Pirellula sp. SH-Sr6A | Sequence length 306 | Average pLDDT 94.38 |
AFDB accessionAF-A0A165ADY9-F1 | Description Site-specific recombinase phage integrase family Site-specific recombinase phage integrase family ... Site-specific recombinase phage integrase family | SpeciesBacillus subtilis Bacillus subtilis | Sequence length 333 | Average pLDDT 94.31 |
AFDB accessionAF-A0A7Z1KDL2-F1 | Description Recombinase Recombinase | SpeciesBacillus pseudomycoides Bacillus pseudomycoides | Sequence length 334 | Average pLDDT 94.25 |
AFDB accessionAF-A0A2A5IKQ0-F1 | Description Recombinase Recombinase | SpeciesBacillus pumilus Bacillus pumilus | Sequence length 333 | Average pLDDT 94.25 |
AFDB accessionAF-A0A410WH81-F1 | Description Site-specific integrase Site-specific integrase | SpeciesBacillus vallismortis Bacillus vallismortis | Sequence length 333 | Average pLDDT 94.19 |
AFDB accessionAF-A0A6H0WKB9-F1 | Description Tyrosine-type recombinase/integrase Tyrosine-type recombinase/integrase | SpeciesBacillus tequilensis Bacillus tequilensis | Sequence length 335 | Average pLDDT 94.06 |
AFDB accessionAF-W7YGJ9-F1 | Description Uncharacterized protein Uncharacterized protein | SpeciesPaenibacillus pini JCM 16418 Paenibacillus pini JCM 16418 | Sequence length 334 | Average pLDDT 94.06 |
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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.
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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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