Histidine--tRNA ligase
AF-Q9HLX5-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-A0A6G2HFL5-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalorubrum sp. JWXQ-INN 858 Halorubrum sp. JWXQ-INN 858 | Sequence length 438 | Average pLDDT 95.38 |
AFDB accessionAF-E4NLG2-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalogeometricum borinquense (strain ATCC 700274 / DSM 11551 / JCM 10706 / KCTC 4070 / PR3) Halogeometricum borinquense (strain ATCC 700274 / DSM 11551 / JCM 10706 / KCTC 4070 / PR3)... Halogeometricum borinquense (strain ATCC 700274 / DSM 11551 / JCM 10706 / KCTC 4070 / PR3) | Sequence length 431 | Average pLDDT 95.31 |
AFDB accessionAF-M0DEV8-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalogeometricum pallidum JCM 14848 Halogeometricum pallidum JCM 14848 | Sequence length 431 | Average pLDDT 95.31 |
AFDB accessionAF-Q3IMP5-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesNatronomonas pharaonis (strain ATCC 35678 / DSM 2160 / CIP 103997 / JCM 8858 / NBRC 14720 / NCIMB 2260 / Gabara) Natronomonas pharaonis (strain ATCC 35678 / DSM 2160 / CIP 103997 / JCM 8858 / NBRC 14720 / NCIMB 2260 / Gabara)... Natronomonas pharaonis (strain ATCC 35678 / DSM 2160 / CIP 103997 / JCM 8858 / NBRC 14720 / NCIMB 2260 / Gabara) | Sequence length 432 | Average pLDDT 95.28 |
AFDB accessionAF-Q18DQ2-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHaloquadratum walsbyi (strain DSM 16790 / HBSQ001) Haloquadratum walsbyi (strain DSM 16790 / HBSQ001)... Haloquadratum walsbyi (strain DSM 16790 / HBSQ001) | Sequence length 434 | Average pLDDT 95.28 |
AFDB accessionAF-A0A256J6X1-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalorubrum ezzemoulense Halorubrum ezzemoulense | Sequence length 440 | Average pLDDT 95.25 |
AFDB accessionAF-M0D9H0-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalorubrum terrestre JCM 10247 Halorubrum terrestre JCM 10247 | Sequence length 440 | Average pLDDT 95.25 |
AFDB accessionAF-M0NMF6-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalorubrum litoreum JCM 13561 Halorubrum litoreum JCM 13561 | Sequence length 440 | Average pLDDT 95.25 |
AFDB accessionAF-B9LRS2-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34) Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)... Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34) | Sequence length 442 | Average pLDDT 95.24 |
AFDB accessionAF-A0A256KNF0-F1 | Description Histidine--tRNA ligase Histidine--tRNA ligase | SpeciesHalorubrum distributum Halorubrum distributum | Sequence length 440 | Average pLDDT 95.19 |
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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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