Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	A	E	R	K	F	L	F	A	C	L	I	F	A	L	V	I	Y	A	I	H	A	F	G	L	F	D	L	L	T	D	L	P	H	L	Q	T	L	I	R	Q	S	G	F	F	G	Y	S	L	Y	I	L	L	F	I	I	A	T	L
Secondary structure
SS confidence
Disorder		?	?	?	?																								?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	L	L	P	G	S	I	L	V	I	A	G	G	I	V	F	G	P	L	L	G	T	L	L	S	L	I	A	A	T	L	A	S	S	C	S	F	L	L	A	R	W	L	G	R	D	L	L	L	K	Y	V	G	H	S	N	T	F	Q	A
Secondary structure
SS confidence
Disorder			?	?	?																																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	E	K	G	I	A	R	N	G	I	D	F	L	I	L	T	R	L	I	P	L	F	P	Y	N	I	Q	N	Y	A	Y	G	L	T	T	I	A	F	W	P	Y	T	L	I	S	A	L	T	T	L	P	G	I	V	I	Y	T	V	M	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.
Sequence		S	D	L	A	N	E	G	I	T	L	R	F	I	L	Q	L	C	L	A	G	L	A	L	F	I	L	V	Q	L	A	K	L	Y	A	R	H	K	H	V	D	L	S	A	S	R	R	S	P	L	T	H	P	K	N	E	G
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 3p5n chain A Region: 64 - 95 Aligned: 32 Modelled: 32 Confidence: 66.0% Identity: 19% PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter Phyre2 PDB 3rko chain M Region: 11 - 150 Aligned: 137 Modelled: 140 Confidence: 35.2% Identity: 11% PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2bbj chain B Region: 159 - 217 Aligned: 51 Modelled: 59 Confidence: 26.3% Identity: 14% 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 2iub chain A domain 2 Region: 159 - 218 Aligned: 44 Modelled: 45 Confidence: 14.0% Identity: 14% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 3rko chain N Region: 7 - 156 Aligned: 144 Modelled: 150 Confidence: 9.4% Identity: 12% PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 1f6g chain A Region: 1 - 128 Aligned: 124 Modelled: 128 Confidence: 9.2% Identity: 10% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 1cii chain A Region: 116 - 185 Aligned: 65 Modelled: 70 Confidence: 7.0% Identity: 11% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 1pw4 chain A Region: 159 - 224 Aligned: 66 Modelled: 66 Confidence: 6.5% Identity: 11% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2jln chain A Region: 31 - 236 Aligned: 193 Modelled: 206 Confidence: 6.4% Identity: 17% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 1iij chain A Region: 157 - 183 Aligned: 27 Modelled: 27 Confidence: 5.9% Identity: 7% PDB header:signaling protein Chain: A: PDB Molecule:erbb-2 receptor protein-tyrosine kinase; PDBTitle: solution structure of the neu/erbb-2 membrane spanning2 segment Phyre2 PDB 3k3g chain A Region: 38 - 100 Aligned: 63 Modelled: 63 Confidence: 5.4% Identity: 8% PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea Phyre2 PDB 1fft chain B domain 2 Region: 184 - 231 Aligned: 48 Modelled: 48 Confidence: 5.2% Identity: 8% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3dtu chain B domain 2 Region: 181 - 230 Aligned: 50 Modelled: 50 Confidence: 5.2% Identity: 14% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2knc chain A Region: 184 - 234 Aligned: 51 Modelled: 51 Confidence: 5.0% Identity: 10% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 1 c3p5nA_ 2 c3rkoM_ 3 c2bbjB_ 4 d2iuba2 5 c3rkoN_ 6 d1f6ga_ 7 c1ciiA_ 8 d1pw4a_ 9 c2jlnA_ 10 c1iijA_ 11 c3k3gA_ 12 d1fftb2 13 d3dtub2 14 c2kncA_

Detailed template information

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

1 c3p5nA_ 66.0 19 PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter 2 c3rkoM_ 35.2 11 PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 3 c2bbjB_ 26.3 14 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 4 d2iuba2 14.0 14 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 5 c3rkoN_ 9.4 12 PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 6 d1f6ga_ 9.2 10 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 7 c1ciiA_ 7.0 11 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 8 d1pw4a_ 6.5 11 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 9 c2jlnA_ 6.4 17 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 10 c1iijA_ 5.9 7 PDB header:signaling protein Chain: A: PDB Molecule:erbb-2 receptor protein-tyrosine kinase; PDBTitle: solution structure of the neu/erbb-2 membrane spanning2 segment 11 c3k3gA_ 5.4 8 PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea 12 d1fftb2 5.2 8 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 13 d3dtub2 5.2 14 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 14 c2kncA_ 5.0 10 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

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