Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	C	S	A	D	E	T	P	V	C	C	C	M	D	V	G	T	I	M	D	N	S	D	C	T	A	S	Y	S	R	V	F	A	N	R	A	E	A	E	Q	T	L	A	A	L	T	E	K	A	R	S	V	E	S	E	P	C	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																											?																			?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.
Sequence		I	T	P	T	F	T	E	E	S	D	G	V	R	L	D	I	D	F	T	F	A	C	E	A	E	M	L	I	F	Q	L	G	L	R
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 2k3i chain A Region: 3 - 94 Aligned: 92 Modelled: 92 Confidence: 100.0% Identity: 40% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yiis; PDBTitle: solution nmr structure of protein yiis from shigella2 flexneri. northeast structural genomics consortium target3 sfr90 Phyre2 PDB 2jz5 chain A Region: 14 - 94 Aligned: 79 Modelled: 81 Confidence: 100.0% Identity: 30% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein vpa0419; PDBTitle: nmr solution structure of protein vpa0419 from vibrio2 parahaemolyticus. northeast structural genomics target3 vpr68 Phyre2 PDB 2khd chain A Region: 1 - 94 Aligned: 91 Modelled: 94 Confidence: 100.0% Identity: 31% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein vc_a0919; PDBTitle: solution nmr structure of vc_a0919 from vibrio cholerae.2 northeast structural genomics consortium target vcr52 Phyre2 PDB 2o6n chain A Region: 38 - 54 Aligned: 17 Modelled: 17 Confidence: 22.0% Identity: 29% PDB header:de novo protein Chain: A: PDB Molecule:rh4b designed peptide; PDBTitle: rh4b: designed right-handed coiled coil tetramer with all biological2 amino acids Phyre2 PDB 1urz chain C Region: 57 - 92 Aligned: 33 Modelled: 36 Confidence: 15.9% Identity: 21% PDB header:virus/viral protein Chain: C: PDB Molecule:envelope protein; PDBTitle: low ph induced, membrane fusion conformation of the2 envelope protein of tick-borne encephalitis virus Phyre2 PDB 2yxy chain A Region: 36 - 55 Aligned: 20 Modelled: 20 Confidence: 15.1% Identity: 50% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical conserved protein, gk0453; PDBTitle: crystarl structure of hypothetical conserved protein, gk0453 Phyre2 PDB 2k8e chain A Region: 20 - 76 Aligned: 51 Modelled: 57 Confidence: 10.6% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0339 protein yegp; PDBTitle: solution nmr structure of protein of unknown function yegp from e.2 coli. ontario center for structural proteomics target ec0640_1_1233 northeast structural genomics consortium target et102. Phyre2 PDB 3i08 chain D Region: 21 - 50 Aligned: 30 Modelled: 30 Confidence: 10.0% Identity: 27% PDB header:signaling protein Chain: D: PDB Molecule:neurogenic locus notch homolog protein 1; PDBTitle: crystal structure of the s1-cleaved notch1 negative2 regulatory region (nrr) Phyre2 PDB 3d3r chain A domain 1 Region: 36 - 55 Aligned: 20 Modelled: 20 Confidence: 10.0% Identity: 30% Fold: OB-fold Superfamily: HupF/HypC-like Family: HupF/HypC-like Phyre2 PDB 1sf9 chain A Region: 36 - 55 Aligned: 20 Modelled: 20 Confidence: 9.4% Identity: 40% Fold: SH3-like barrel Superfamily: Hypothetical protein YfhH Family: Hypothetical protein YfhH Phyre2 PDB 3uaj chain A Region: 18 - 92 Aligned: 38 Modelled: 38 Confidence: 7.5% Identity: 8% PDB header:viral protein/immune system Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure of the envelope glycoprotein ectodomain from dengue2 virus serotype 4 in complex with the fab fragment of the chimpanzee3 monoclonal antibody 5h2 Phyre2 PDB 3d3r chain A Region: 36 - 55 Aligned: 20 Modelled: 20 Confidence: 6.8% Identity: 30% PDB header:chaperone Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf; PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1 Phyre2 1 c2k3iA_ 2 c2jz5A_ 3 c2khdA_ 4 c2o6nA_ 5 c1urzC_ 6 c2yxyA_ 7 c2k8eA_ 8 c3i08D_ 9 d3d3ra1 10 d1sf9a_ 11 c3uajA_ 12 c3d3rA_

Detailed template information

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

1 c2k3iA_ 100.0 40 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yiis; PDBTitle: solution nmr structure of protein yiis from shigella2 flexneri. northeast structural genomics consortium target3 sfr90 2 c2jz5A_ 100.0 30 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein vpa0419; PDBTitle: nmr solution structure of protein vpa0419 from vibrio2 parahaemolyticus. northeast structural genomics target3 vpr68 3 c2khdA_ 100.0 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein vc_a0919; PDBTitle: solution nmr structure of vc_a0919 from vibrio cholerae.2 northeast structural genomics consortium target vcr52 4 c2o6nA_ 22.0 29 PDB header:de novo protein Chain: A: PDB Molecule:rh4b designed peptide; PDBTitle: rh4b: designed right-handed coiled coil tetramer with all biological2 amino acids 5 c1urzC_ 15.9 21 PDB header:virus/viral protein Chain: C: PDB Molecule:envelope protein; PDBTitle: low ph induced, membrane fusion conformation of the2 envelope protein of tick-borne encephalitis virus 6 c2yxyA_ 15.1 50 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical conserved protein, gk0453; PDBTitle: crystarl structure of hypothetical conserved protein, gk0453 7 c2k8eA_ 10.6 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0339 protein yegp; PDBTitle: solution nmr structure of protein of unknown function yegp from e.2 coli. ontario center for structural proteomics target ec0640_1_1233 northeast structural genomics consortium target et102. 8 c3i08D_ 10.0 27 PDB header:signaling protein Chain: D: PDB Molecule:neurogenic locus notch homolog protein 1; PDBTitle: crystal structure of the s1-cleaved notch1 negative2 regulatory region (nrr) 9 d3d3ra1 10.0 30 Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like 10 d1sf9a_ 9.4 40 Fold:SH3-like barrel Superfamily:Hypothetical protein YfhH Family:Hypothetical protein YfhH 11 c3uajA_ 7.5 8 PDB header:viral protein/immune system Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure of the envelope glycoprotein ectodomain from dengue2 virus serotype 4 in complex with the fab fragment of the chimpanzee3 monoclonal antibody 5h2 12 c3d3rA_ 6.8 30 PDB header:chaperone Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf; PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1

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