5'-deoxynucleotidase YfbR
AF-B7UFU9-F1-v4
Share your feedback on structure with Google DeepMind Looks great Could be improved
Information
- 0
- 5
- 10
- 15
- 20
- 25
- 30
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.
Start a structural similarity search to discover similar proteins.
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 |
---|---|---|---|---|
AFDB accessionAF-Q87R72-F1 | Description 5'-deoxynucleotidase VP0926 5'-deoxynucleotidase VP0926 | SpeciesVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)... Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) | Sequence length 194 | Average pLDDT 96.56 |
AFDB accessionAF-Q9KQM0-F1 | Description 5'-deoxynucleotidase VC_1978 5'-deoxynucleotidase VC_1978 | SpeciesVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)... Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) | Sequence length 194 | Average pLDDT 96.47 |
AFDB accessionAF-Q7MMF9-F1 | Description 5'-deoxynucleotidase VV1113 5'-deoxynucleotidase VV1113 | SpeciesVibrio vulnificus (strain YJ016) Vibrio vulnificus (strain YJ016) | Sequence length 194 | Average pLDDT 96.39 |
AFDB accessionAF-G4QGR0-F1 | Description HDc domain-containing protein HDc domain-containing protein | SpeciesGlaciecola nitratireducens (strain JCM 12485 / KCTC 12276 / FR1064) Glaciecola nitratireducens (strain JCM 12485 / KCTC 12276 / FR1064)... Glaciecola nitratireducens (strain JCM 12485 / KCTC 12276 / FR1064) | Sequence length 196 | Average pLDDT 96.38 |
AFDB accessionAF-A0A5P9CK57-F1 | Description 5'-deoxynucleotidase YfbR 5'-deoxynucleotidase YfbR | SpeciesVibrio aquimaris Vibrio aquimaris | Sequence length 197 | Average pLDDT 96.38 |
AFDB accessionAF-A0A2N1HR85-F1 | Description 5'-deoxynucleotidase 5'-deoxynucleotidase | SpeciesGlaciecola sp. 33A Glaciecola sp. 33A | Sequence length 196 | Average pLDDT 96.38 |
AFDB accessionAF-Q8EEA3-F1 | Description 5'-deoxynucleotidase SO_2484 5'-deoxynucleotidase SO_2484 | SpeciesShewanella oneidensis (strain MR-1) Shewanella oneidensis (strain MR-1) | Sequence length 195 | Average pLDDT 96.32 |
AFDB accessionAF-A0A7Y4EA06-F1 | Description 5'-deoxynucleotidase 5'-deoxynucleotidase | SpeciesVibrio sp. RE88 Vibrio sp. RE88 | Sequence length 199 | Average pLDDT 96.31 |
AFDB accessionAF-A0A1G2R782-F1 | Description HDc domain-containing protein HDc domain-containing protein | SpeciesCandidatus Wildermuthbacteria bacterium RIFCSPHIGHO2_02_FULL_48_16 Candidatus Wildermuthbacteria bacterium RIFCSPHIGHO2_02_FULL_48_16... Candidatus Wildermuthbacteria bacterium RIFCSPHIGHO2_02_FULL_48_16 | Sequence length 181 | Average pLDDT 96.31 |
AFDB accessionAF-A0A2N7FJ89-F1 | Description 5'-deoxynucleotidase 5'-deoxynucleotidase | SpeciesVibrio splendidus Vibrio splendidus | Sequence length 198 | Average pLDDT 96.25 |
Visit our online training course
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
Data is available for academic and commercial use, under a CC-BY-4.0 licence.
EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice.
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.
Feedback and questions
If you want to share feedback on an AlphaFold structure prediction, consider using the feedback buttons at the top of each structure page. If you have any questions that are not covered in the FAQs, please contact alphafold@deepmind.com. If you have feedback on the website or experience any bugs please contact afdbhelp@ebi.ac.uk.
Let us know how the AlphaFold Protein Structure Database has been useful in your research at alphafold@deepmind.com.
Disclaimer
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.
Use of the AlphaFold Protein Structure Database is subject to EMBL-EBI Terms of Use.