Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.
Sequence		M	I	R	K	Y	W	W	L	V	V	F	A	V	F	V	F	L	F	D	T	L	L	M	Q	W	I	E	L	L	A	T	E	T	D	K	C	R	N	M	N	S	V	N	P	L	K	L	V	N	C	D	E	L	N	F	Q	D	R	M
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 1xme chain C domain 1 Region: 6 - 14 Aligned: 9 Modelled: 9 Confidence: 12.5% Identity: 67% Fold: Single transmembrane helix Superfamily: Bacterial ba3 type cytochrome c oxidase subunit IIa Family: Bacterial ba3 type cytochrome c oxidase subunit IIa Phyre2 PDB 2xfc chain D Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 12.3% Identity: 45% PDB header:virus Chain: D: PDB Molecule:e1 envelope glycoprotein; PDBTitle: the chikungunya e1 e2 envelope glycoprotein complex fit into2 the semliki forest virus cryo-em map Phyre2 PDB 2xfb chain F Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 12.2% Identity: 45% PDB header:virus Chain: F: PDB Molecule:e1 envelope glycoprotein; PDBTitle: the chikungunya e1 e2 envelope glycoprotein complex fit into2 the sindbis virus cryo-em map Phyre2 PDB 3n42 chain F Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 12.0% Identity: 45% PDB header:viral protein Chain: F: PDB Molecule:e1 envelope glycoprotein; PDBTitle: crystal structures of the mature envelope glycoprotein complex (furin2 cleavage) of chikungunya virus. Phyre2 PDB 1z8y chain E Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 10.3% Identity: 55% PDB header:virus Chain: E: PDB Molecule:spike glycoprotein e1; PDBTitle: mapping the e2 glycoprotein of alphaviruses Phyre2 PDB 3muw chain E Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 10.1% Identity: 55% PDB header:virus Chain: E: PDB Molecule:structural polyprotein; PDBTitle: pseudo-atomic structure of the e2-e1 protein shell in sindbis virus Phyre2 PDB 1ld4 chain O Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 10.0% Identity: 55% PDB header:virus Chain: O: PDB Molecule:spike glycoprotein e1; PDBTitle: placement of the structural proteins in sindbis virus Phyre2 PDB 2ala chain A domain 2 Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 9.6% Identity: 36% Fold: Viral glycoprotein, central and dimerisation domains Superfamily: Viral glycoprotein, central and dimerisation domains Family: Viral glycoprotein, central and dimerisation domains Phyre2 PDB 3j0c chain G Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 8.6% Identity: 36% PDB header:virus Chain: G: PDB Molecule:e1 envelope glycoprotein; PDBTitle: models of e1, e2 and cp of venezuelan equine encephalitis virus tc-832 strain restrained by a near atomic resolution cryo-em map Phyre2 PDB 2ala chain A Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 8.4% Identity: 36% PDB header:viral protein Chain: A: PDB Molecule:structural polyprotein (p130); PDBTitle: crystal structure of the semliki forest virus envelope protein e1 in2 its monomeric conformation. Phyre2 PDB 1q90 chain A domain 3 Region: 7 - 22 Aligned: 16 Modelled: 16 Confidence: 8.3% Identity: 50% Fold: Single transmembrane helix Superfamily: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor Family: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor Phyre2 PDB 3muu chain A Region: 41 - 51 Aligned: 11 Modelled: 11 Confidence: 6.3% Identity: 55% PDB header:viral protein Chain: A: PDB Molecule:structural polyprotein; PDBTitle: crystal structure of the sindbis virus e2-e1 heterodimer at low ph Phyre2 1 d1xmec1 2 c2xfcD_ 3 c2xfbF_ 4 c3n42F_ 5 c1z8yE_ 6 c3muwE_ 7 c1ld4O_ 8 d2alaa2 9 c3j0cG_ 10 c2alaA_ 11 d1q90a3 12 c3muuA_

Detailed template information

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

1 d1xmec1 12.5 67 Fold:Single transmembrane helix Superfamily:Bacterial ba3 type cytochrome c oxidase subunit IIa Family:Bacterial ba3 type cytochrome c oxidase subunit IIa 2 c2xfcD_ 12.3 45 PDB header:virus Chain: D: PDB Molecule:e1 envelope glycoprotein; PDBTitle: the chikungunya e1 e2 envelope glycoprotein complex fit into2 the semliki forest virus cryo-em map 3 c2xfbF_ 12.2 45 PDB header:virus Chain: F: PDB Molecule:e1 envelope glycoprotein; PDBTitle: the chikungunya e1 e2 envelope glycoprotein complex fit into2 the sindbis virus cryo-em map 4 c3n42F_ 12.0 45 PDB header:viral protein Chain: F: PDB Molecule:e1 envelope glycoprotein; PDBTitle: crystal structures of the mature envelope glycoprotein complex (furin2 cleavage) of chikungunya virus. 5 c1z8yE_ 10.3 55 PDB header:virus Chain: E: PDB Molecule:spike glycoprotein e1; PDBTitle: mapping the e2 glycoprotein of alphaviruses 6 c3muwE_ 10.1 55 PDB header:virus Chain: E: PDB Molecule:structural polyprotein; PDBTitle: pseudo-atomic structure of the e2-e1 protein shell in sindbis virus 7 c1ld4O_ 10.0 55 PDB header:virus Chain: O: PDB Molecule:spike glycoprotein e1; PDBTitle: placement of the structural proteins in sindbis virus 8 d2alaa2 9.6 36 Fold:Viral glycoprotein, central and dimerisation domains Superfamily:Viral glycoprotein, central and dimerisation domains Family:Viral glycoprotein, central and dimerisation domains 9 c3j0cG_ 8.6 36 PDB header:virus Chain: G: PDB Molecule:e1 envelope glycoprotein; PDBTitle: models of e1, e2 and cp of venezuelan equine encephalitis virus tc-832 strain restrained by a near atomic resolution cryo-em map 10 c2alaA_ 8.4 36 PDB header:viral protein Chain: A: PDB Molecule:structural polyprotein (p130); PDBTitle: crystal structure of the semliki forest virus envelope protein e1 in2 its monomeric conformation. 11 d1q90a3 8.3 50 Fold:Single transmembrane helix Superfamily:Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor Family:Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor 12 c3muuA_ 6.3 55 PDB header:viral protein Chain: A: PDB Molecule:structural polyprotein; PDBTitle: crystal structure of the sindbis virus e2-e1 heterodimer at low ph

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