Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	T	T	T	P	Q	R	I	G	G	W	L	L	G	P	L	A	W	L	L	V	A	L	L	S	T	T	L	A	L	L	L	Y	T	A	A	L	S	S	P	Q	T	F	Q	T	L	G	G	Q	A	L	T	T	Q	I	L	W	G	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																					?	?	?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	F	I	T	A	I	A	L	W	Y	Y	T	L	W	L	T	I	A	F	F	K	R	R	R	C	V	P	K	H	Y	I	I	W	L	L	I	S	V	L	L	A	V	K	A	F	A	F	S	P	V	E	D	G	I	A	V	R	Q	L	L
Secondary structure
SS confidence
Disorder																																															?	?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.
Sequence		F	T	L	L	A	T	A	L	I	V	P	Y	F	K	R	S	S	R	V	K	A	T	F	V	N	P
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 2k1a chain A Region: 56 - 84 Aligned: 29 Modelled: 29 Confidence: 39.0% Identity: 24% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 2knc chain A Region: 56 - 84 Aligned: 29 Modelled: 29 Confidence: 38.5% Identity: 24% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2bbj chain B Region: 66 - 84 Aligned: 19 Modelled: 19 Confidence: 14.4% Identity: 16% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 2jpn chain A Region: 135 - 142 Aligned: 8 Modelled: 8 Confidence: 13.5% Identity: 50% PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent dna helicase uvsw; PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1 Phyre2 PDB 2lcy chain A Region: 129 - 133 Aligned: 5 Modelled: 5 Confidence: 13.5% Identity: 60% PDB header:viral protein Chain: A: PDB Molecule:virion spike glycoprotein; PDBTitle: nmr structure of the complete internal fusion loop from ebolavirus gp22 at ph 5.5 Phyre2 PDB 2iub chain A domain 2 Region: 64 - 84 Aligned: 21 Modelled: 21 Confidence: 12.9% Identity: 14% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 3csy chain J Region: 129 - 133 Aligned: 5 Modelled: 5 Confidence: 8.6% Identity: 60% PDB header:immune system/viral protein Chain: J: PDB Molecule:envelope glycoprotein gp2; PDBTitle: crystal structure of the trimeric prefusion ebola virus glycoprotein2 in complex with a neutralizing antibody from a human survivor Phyre2 PDB 3s88 chain J Region: 129 - 133 Aligned: 5 Modelled: 5 Confidence: 7.9% Identity: 60% PDB header:immune system/viral protein Chain: J: PDB Molecule:envelope glycoprotein; PDBTitle: crystal structure of sudan ebolavirus glycoprotein (strain gulu) bound2 to 16f6 Phyre2 PDB 1wix chain A Region: 112 - 144 Aligned: 26 Modelled: 33 Confidence: 6.6% Identity: 27% Fold: CH domain-like Superfamily: Hook domain Family: Hook domain Phyre2 PDB 3ehb chain B domain 2 Region: 51 - 103 Aligned: 53 Modelled: 53 Confidence: 6.0% Identity: 23% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 1 c2k1aA_ 2 c2kncA_ 3 c2bbjB_ 4 c2jpnA_ 5 c2lcyA_ 6 d2iuba2 7 c3csyJ_ 8 c3s88J_ 9 d1wixa_ 10 d3ehbb2

Detailed template information

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

1 c2k1aA_ 39.0 24 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 2 c2kncA_ 38.5 24 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 3 c2bbjB_ 14.4 16 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 4 c2jpnA_ 13.5 50 PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent dna helicase uvsw; PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1 5 c2lcyA_ 13.5 60 PDB header:viral protein Chain: A: PDB Molecule:virion spike glycoprotein; PDBTitle: nmr structure of the complete internal fusion loop from ebolavirus gp22 at ph 5.5 6 d2iuba2 12.9 14 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 7 c3csyJ_ 8.6 60 PDB header:immune system/viral protein Chain: J: PDB Molecule:envelope glycoprotein gp2; PDBTitle: crystal structure of the trimeric prefusion ebola virus glycoprotein2 in complex with a neutralizing antibody from a human survivor 8 c3s88J_ 7.9 60 PDB header:immune system/viral protein Chain: J: PDB Molecule:envelope glycoprotein; PDBTitle: crystal structure of sudan ebolavirus glycoprotein (strain gulu) bound2 to 16f6 9 d1wixa_ 6.6 27 Fold:CH domain-like Superfamily:Hook domain Family:Hook domain 10 d3ehbb2 6.0 23 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region

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