Spermidine/putrescine transport system substrate-binding protein
AF-A0A1N7HGE5-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.
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-A0A509C952-F1 | Description Spermidine/putrescine-binding periplasmic protein Spermidine/putrescine-binding periplasmic protein ... Spermidine/putrescine-binding periplasmic protein | SpeciesSalmonella sp. NCTC 6947 Salmonella sp. NCTC 6947 | Sequence length 254 | Average pLDDT 97.5 |
AFDB accessionAF-A0A378BDH8-F1 | Description ABC transporter ABC transporter | SpeciesKlebsiella pneumoniae Klebsiella pneumoniae | Sequence length 235 | Average pLDDT 97.5 |
AFDB accessionAF-A0A382EL18-F1 | Description Uncharacterized protein Uncharacterized protein | Speciesmarine metagenome marine metagenome | Sequence length 231 | Average pLDDT 96.94 |
AFDB accessionAF-A0A3M5T3L6-F1 | Description Polyamine ABC transporter, periplasmic polyamine-binding protein Polyamine ABC transporter, periplasmic polyamine-binding protein ... Polyamine ABC transporter, periplasmic polyamine-binding protein | SpeciesPseudomonas savastanoi pv. glycinea Pseudomonas savastanoi pv. glycinea | Sequence length 270 | Average pLDDT 96.81 |
AFDB accessionAF-A0A023RSH2-F1 | Description ABC-type sulfate transport system, periplasmic component ABC-type sulfate transport system, periplasmic component ... ABC-type sulfate transport system, periplasmic component | SpeciesAeromonas media WS Aeromonas media WS | Sequence length 310 | Average pLDDT 96.75 |
AFDB accessionAF-A0A529KME4-F1 | Description Spermidine/putrescine ABC transporter substrate-binding protein Spermidine/putrescine ABC transporter substrate-binding protein ... Spermidine/putrescine ABC transporter substrate-binding protein | SpeciesMesorhizobium sp Mesorhizobium sp | Sequence length 290 | Average pLDDT 96.75 |
AFDB accessionAF-A0A3S2F324-F1 | Description Sulfate ABC transporter substrate-binding protein Sulfate ABC transporter substrate-binding protein ... Sulfate ABC transporter substrate-binding protein | SpeciesMesorhizobium sp. M7A.F.Ca.AU.002.06.1.1 Mesorhizobium sp. M7A.F.Ca.AU.002.06.1.1... Mesorhizobium sp. M7A.F.Ca.AU.002.06.1.1 | Sequence length 282 | Average pLDDT 96.69 |
AFDB accessionAF-A0A2N7SIC1-F1 | Description Polyamine ABC transporter substrate-binding protein Polyamine ABC transporter substrate-binding protein ... Polyamine ABC transporter substrate-binding protein | SpeciesMesorhizobium intechi Mesorhizobium intechi | Sequence length 314 | Average pLDDT 96.69 |
AFDB accessionAF-A0A0U3SYK4-F1 | Description Sulfate transporter Sulfate transporter | Speciesuncultured bacterium 3 uncultured bacterium 3 | Sequence length 253 | Average pLDDT 96.62 |
AFDB accessionAF-A0A376L821-F1 | Description Spermidine/putrescine ABC transporter substrate-binding protein Spermidine/putrescine ABC transporter substrate-binding protein ... Spermidine/putrescine ABC transporter substrate-binding protein | SpeciesEscherichia coli Escherichia coli | Sequence length 235 | Average pLDDT 96.62 |
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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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