Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.
Sequence		M	K	E	N	K	V	Q	Q	I	S	H	K	L	I	N	I	V	V	F	V	A	I	V	E	Y	A	Y	L	F	L	H	F	Y
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 2ovc chain A Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 27.3% Identity: 64% PDB header:transport protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily kqt member 4; PDBTitle: crystal structure of a coiled-coil tetramerization domain from kv7.42 channels Phyre2 PDB 1bde chain A Region: 28 - 32 Aligned: 5 Modelled: 5 Confidence: 7.2% Identity: 80% PDB header:aids Chain: A: PDB Molecule:vpr protein; PDBTitle: helical structure of polypeptides from the c-terminal half2 of hiv-1 vpr, nmr, 20 structures Phyre2 PDB 1x9v chain A Region: 28 - 32 Aligned: 5 Modelled: 5 Confidence: 6.2% Identity: 80% PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: dimeric structure of the c-terminal domain of vpr Phyre2 PDB 1vry chain A Region: 16 - 26 Aligned: 11 Modelled: 11 Confidence: 5.8% Identity: 55% PDB header:membrane protein Chain: A: PDB Molecule:glycine receptor alpha-1 chain; PDBTitle: second and third transmembrane domains of the alpha-12 subunit of human glycine receptor Phyre2 1 c2ovcA_ 2 c1bdeA_ 3 c1x9vA_ 4 c1vryA_

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2ovcA_ 27.3 64 PDB header:transport protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily kqt member 4; PDBTitle: crystal structure of a coiled-coil tetramerization domain from kv7.42 channels 2 c1bdeA_ 7.2 80 PDB header:aids Chain: A: PDB Molecule:vpr protein; PDBTitle: helical structure of polypeptides from the c-terminal half2 of hiv-1 vpr, nmr, 20 structures 3 c1x9vA_ 6.2 80 PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: dimeric structure of the c-terminal domain of vpr 4 c1vryA_ 5.8 55 PDB header:membrane protein Chain: A: PDB Molecule:glycine receptor alpha-1 chain; PDBTitle: second and third transmembrane domains of the alpha-12 subunit of human glycine receptor

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0