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Alpha-aminoadipic semialdehyde dehydrogenase

Reviewed
Reference proteome

AF-P49419-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

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Information

Structure viewer
 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.

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SequenceNo structure available
Structure Tools
  • 8:03:42
    Mol* Plugin 4.5.0 [8/22/2024, 2:35:37 PM]
 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.

Hide colour legend

Scored residueAligned residue
01002003004005000100200300400500
  • 0
  • 5
  • 10
  • 15
  • 20
  • 25
  • 30
Expected position error (Ångströms)

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.

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153950100150200250300350400450500200400
50100150200250300350400450500GAVLISTCMDNEQRKHFYWPGAVLISTCMDNEQRKHFYWPAlternative amino acidsResidue sequence number
BenignUncertainPathogenic Reference
Amino acid present in the reference UniProt protein sequence, based on HG38
  • 0.0
  • 0.2
  • 0.3
  • 0.4
  • 0.5
  • 0.6
  • 0.7
  • 0.8
  • 1.0
  • -
Filter by category
0
0.34
0.00.34
0.34
0.56
0.340.564
0.56
1
0.5641
Similar structures Discover similar structures from the Protein Data Bank (PDB) and the AlphaFold Database clustered to 50% sequence identity (AFDB50) using Foldseek.
PDB ID
and chain
DescriptionSpecies 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
Align in 3D
PDB ID and
chain
2j6l_G_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
1.29e-101
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2j6l_E_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
1.82e-101
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2j6l_D_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
5.32e-101
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2j6l_F_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
1.24e-100
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2j6l_A_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
1.47e-100
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2j6l_H_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
2.32e-100
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2j6l_C_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
2.59e-100
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2j6l_B_1
Description

Alpha-aminoadipic semialdehyde dehydrogenase

Alpha-aminoadipic semialdeh...

Alpha-aminoadipic semialdehyde dehydrogenase
Species

Homo sapiens

Homo sapiens

Residue range

29 - 527P49419

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.
9.00e-100
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
99.7%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
1.30
Align in 3D
PDB ID and
chain
2jg7_G_1
Description

aldehyde dehydrogenase (NAD(+))

aldehyde dehydrogenase (NAD...

aldehyde dehydrogenase (NAD(+))
Species

Acanthopagrus schlegelii

Acanthopagrus schlegelii

Residue range

2 - 511Q4KTQ7

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.
4.62e-96
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
85.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.83
Align in 3D
PDB ID and
chain
2jg7_E_1
Description

aldehyde dehydrogenase (NAD(+))

aldehyde dehydrogenase (NAD...

aldehyde dehydrogenase (NAD(+))
Species

Acanthopagrus schlegelii

Acanthopagrus schlegelii

Residue range

2 - 511Q4KTQ7

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.
1.21e-95
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
85.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.83
Items per page:
1 – 10 of 969
AF-P49419-F1
Current entry

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Aligned in 3D
Rotate and zoom structures in the 3D
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.
Toggle structures in both PDB and AFDB tables to view and align them with the entry structure in the 3D viewer. You can also download the aligned coordinates of the toggled structures and the entry structure.
Structure similarity clusterPredicted structures in the AlphaFold Protein Structure Database clustered using MMseqs2 and Foldseek. This data is provided by the AFDB Clusters.

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 DescriptionSpecies
Sequence length
Average pLDDT
AFDB accessionAF-E1JCY2-F1
Unreviewed
Reference proteome
Description Gamma-aminobutyraldehyde dehydrogenase

Gamma-aminobutyraldehyde dehydrogenase ...

Gamma-aminobutyraldehyde dehydrogenase
SpeciesEscherichia coli MS 124-1
Escherichia coli MS 124-1
Sequence length 430 Average pLDDT 98.69
AFDB accessionAF-H7GHL2-F1
Unreviewed
Reference proteome
Description 1-pyrroline-5-carboxylate dehydrogenase

1-pyrroline-5-carboxylate dehydrogenase ...

1-pyrroline-5-carboxylate dehydrogenase
SpeciesThermus parvatiensis
Thermus parvatiensis
Sequence length 516 Average pLDDT 98.69
AFDB accessionAF-A0A3P4ANH6-F1
Unreviewed
Reference proteome
Description 1-pyrroline-5-carboxylate dehydrogenase 1

1-pyrroline-5-carboxylate dehydrogenase 1 ...

1-pyrroline-5-carboxylate dehydrogenase 1
SpeciesThermus thermophilus
Thermus thermophilus
Sequence length 516 Average pLDDT 98.69
AFDB accessionAF-B1XDF5-F1
Reviewed (Swiss-Prot)
Description Gamma-aminobutyraldehyde dehydrogenase

Gamma-aminobutyraldehyde dehydrogenase ...

Gamma-aminobutyraldehyde dehydrogenase
SpeciesEscherichia coli (strain K12 / DH10B)

Escherichia coli (strain K12 / DH10B)...

Escherichia coli (strain K12 / DH10B)
Sequence length 474 Average pLDDT 98.69
AFDB accessionAF-C4ZVI3-F1
Reviewed (Swiss-Prot)
Description Gamma-aminobutyraldehyde dehydrogenase

Gamma-aminobutyraldehyde dehydrogenase ...

Gamma-aminobutyraldehyde dehydrogenase
SpeciesEscherichia coli (strain K12 / MC4100 / BW2952)

Escherichia coli (strain K12 / MC4100 / BW2952)...

Escherichia coli (strain K12 / MC4100 / BW2952)
Sequence length 474 Average pLDDT 98.69
AFDB accessionAF-F6DE66-F1
Unreviewed
Reference proteome
Description Delta-1-pyrroline-5-carboxylate dehydrogenase

Delta-1-pyrroline-5-carboxylate dehydrogenase ...

Delta-1-pyrroline-5-carboxylate dehydrogenase
SpeciesThermus thermophilus (strain SG0.5JP17-16)

Thermus thermophilus (strain SG0.5JP17-16)...

Thermus thermophilus (strain SG0.5JP17-16)
Sequence length 516 Average pLDDT 98.69
AFDB accessionAF-A0A1J1EVC3-F1
Unreviewed
Reference proteome
Description Delta-1-pyrroline-5-carboxylate dehydrogenase

Delta-1-pyrroline-5-carboxylate dehydrogenase ...

Delta-1-pyrroline-5-carboxylate dehydrogenase
SpeciesThermus thermophilus
Thermus thermophilus
Sequence length 516 Average pLDDT 98.69
AFDB accessionAF-A0A376RKJ2-F1
Unreviewed
Reference proteome
Description Gamma-aminobutyraldehyde dehydrogenase

Gamma-aminobutyraldehyde dehydrogenase ...

Gamma-aminobutyraldehyde dehydrogenase
SpeciesEscherichia coli
Escherichia coli
Sequence length 430 Average pLDDT 98.69
AFDB accessionAF-A2VYT6-F1
Unreviewed
Reference proteome
Description Succinate-semialdehyde dehydrogenase (NAD(P)+)

Succinate-semialdehyde dehydrogenase (NAD(P)+) ...

Succinate-semialdehyde dehydrogenase (NAD(P)+)
SpeciesBurkholderia cenocepacia PC184
Burkholderia cenocepacia PC184
Sequence length 453 Average pLDDT 98.69
AFDB accessionAF-H9ZPW5-F1
Unreviewed
Reference proteome
Description Delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative

Delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative ...

Delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative
SpeciesThermus thermophilus JL-18
Thermus thermophilus JL-18
Sequence length 516 Average pLDDT 98.69
Items per page:
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Help

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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.

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:

  • We’re confident in the relative position of residue 200
  • We’re not confident in the relative position of residue 600

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.

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.

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).

 


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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