Kynurenine formamidase
AF-Q8K4H1-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 chain4e15_A_1 | Description Kynurenine formamidase Kynurenine formamidase | Species Drosophila melanogaster Drosophila melanogaster | Residue range 1 - 300Q9VMC9 | 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 25.4% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.50 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 chain4e15_B_1 | Description Kynurenine formamidase Kynurenine formamidase | Species Drosophila melanogaster Drosophila melanogaster | Residue range 1 - 300Q9VMC9 | 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 25% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.50 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 chain2pbl_D_1 | Description Alpha/beta hydrolase fold-3 domain-containing protein Alpha/beta hydrolase fold-3... Alpha/beta hydrolase fold-3 domain-containing protein | Species Ruegeria sp. (strain TM1040) Ruegeria sp. (strain TM1040... Ruegeria sp. (strain TM1040) | Residue range 1 - 261Q1GDP2 | 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 24.6% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.79 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 chain2pbl_A_1 | Description Alpha/beta hydrolase fold-3 domain-containing protein Alpha/beta hydrolase fold-3... Alpha/beta hydrolase fold-3 domain-containing protein | Species Ruegeria sp. (strain TM1040) Ruegeria sp. (strain TM1040... Ruegeria sp. (strain TM1040) | Residue range 1 - 261Q1GDP2 | 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 24.9% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.79 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 chain2pbl_C_1 | Description Alpha/beta hydrolase fold-3 domain-containing protein Alpha/beta hydrolase fold-3... Alpha/beta hydrolase fold-3 domain-containing protein | Species Ruegeria sp. (strain TM1040) Ruegeria sp. (strain TM1040... Ruegeria sp. (strain TM1040) | Residue range 1 - 261Q1GDP2 | 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 24.8% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.79 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 chain2pbl_B_1 | Description Alpha/beta hydrolase fold-3 domain-containing protein Alpha/beta hydrolase fold-3... Alpha/beta hydrolase fold-3 domain-containing protein | Species Ruegeria sp. (strain TM1040) Ruegeria sp. (strain TM1040... Ruegeria sp. (strain TM1040) | Residue range 1 - 261Q1GDP2 | 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 24.4% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.79 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 chain4zrs_A_1 | Description BD-FAE-like domain-containing protein BD-FAE-like domain-containi... BD-FAE-like domain-containing protein | Species uncultured bacterium uncultured bacterium | Residue range 1 - 290E7DJY5 | 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 21.2% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.00 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 chain4zrs_B_1 | Description BD-FAE-like domain-containing protein BD-FAE-like domain-containi... BD-FAE-like domain-containing protein | Species uncultured bacterium uncultured bacterium | Residue range 1 - 290E7DJY5 | 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 21.5% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.00 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 chain2yh2_A_1 | Description Alpha/beta hydrolase fold-3 domain-containing protein Alpha/beta hydrolase fold-3... Alpha/beta hydrolase fold-3 domain-containing protein | Species Pyrobaculum calidifontis Pyrobaculum calidifontis | Residue range 1 - 313Q8NKS0 | 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 17.6% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 2.20 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 chain3aio_B_1 | Description Alpha/beta hydrolase fold-3 domain-containing protein Alpha/beta hydrolase fold-3... Alpha/beta hydrolase fold-3 domain-containing protein | Species Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) Sulfurisphaera tokodaii (st... Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) | Residue range 1 - 303Q976W8 | 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 17.5% Percentage of identical residues between aligned sequences over the aligned length. | Resolution (Å) 1.70 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-A0A5N9ENP5-F1 | Description Alpha/beta hydrolase Alpha/beta hydrolase | SpeciesSAR202 cluster bacterium SAR202 cluster bacterium | Sequence length 245 | Average pLDDT 98.38 |
AFDB accessionAF-A0A3A8HW82-F1 | Description Hydrolase_4 domain-containing protein Hydrolase_4 domain-containing protein ... Hydrolase_4 domain-containing protein | SpeciesCorallococcus sp. CA054B Corallococcus sp. CA054B | Sequence length 241 | Average pLDDT 97.81 |
AFDB accessionAF-A0A3A8TUC4-F1 | Description Hydrolase_4 domain-containing protein Hydrolase_4 domain-containing protein ... Hydrolase_4 domain-containing protein | SpeciesCorallococcus sp. AB038B Corallococcus sp. AB038B | Sequence length 241 | Average pLDDT 97.75 |
AFDB accessionAF-A0A7X4YAL2-F1 | Description DLH domain-containing protein DLH domain-containing protein | SpeciesCorallococcus exiguus Corallococcus exiguus | Sequence length 241 | Average pLDDT 97.75 |
AFDB accessionAF-A0A3A8J6Q8-F1 | Description Hydrolase_4 domain-containing protein Hydrolase_4 domain-containing protein ... Hydrolase_4 domain-containing protein | SpeciesCorallococcus sp. CA049B Corallococcus sp. CA049B | Sequence length 241 | Average pLDDT 97.69 |
AFDB accessionAF-A0A3A8SGI2-F1 | Description AB hydrolase-1 domain-containing protein AB hydrolase-1 domain-containing protein ... AB hydrolase-1 domain-containing protein | SpeciesCorallococcus sp. AB032C Corallococcus sp. AB032C | Sequence length 241 | Average pLDDT 97.69 |
AFDB accessionAF-A0A3A8GDL1-F1 | Description Alpha/beta fold hydrolase Alpha/beta fold hydrolase | SpeciesCorallococcus sp. AB011P Corallococcus sp. AB011P | Sequence length 241 | Average pLDDT 97.69 |
AFDB accessionAF-A0A0F6WGE1-F1 | Description Esterase Esterase | Speciesuncultured bacterium uncultured bacterium | Sequence length 297 | Average pLDDT 97.62 |
AFDB accessionAF-A0A2W4CQL2-F1 | Description Esterase Esterase | SpeciesRhizobium tubonense Rhizobium tubonense | Sequence length 272 | Average pLDDT 97.56 |
AFDB accessionAF-A0A1V9QPK1-F1 | Description Acetylesterase Acetylesterase | SpeciesLigilactobacillus salivarius Ligilactobacillus salivarius | Sequence length 273 | Average pLDDT 97.56 |
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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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AlphaMissense Copyright (2023) DeepMind Technologies Limited.
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