Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	L	A	T	A	L	L	I	V	G	L	L	L	V	V	Y	S	A	D	R	L	V	F	A	A	S	I	L	C	R	T	F	G	I	P	P	L	I	I	G	M	T	V	V	S	I	G	T	S	L	P	E	V	I	V	S	L	A	A
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	L	H	E	Q	R	D	L	A	V	G	T	A	L	G	S	N	I	I	N	I	L	L	I	L	G	L	A	A	L	V	R	P	F	T	V	H	S	D	V	L	R	R	E	L	P	L	M	L	L	V	S	V	V	A	G	S	V	L	Y
Secondary structure
SS confidence
Disorder			?	?	?	?	?																														?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	G	Q	L	S	R	S	D	G	I	F	L	L	F	L	A	V	L	W	L	L	F	I	V	K	L	A	R	Q	A	E	R	Q	G	T	D	S	L	T	R	E	Q	L	A	E	L	P	R	D	G	G	L	P	V	A	F	L	W	L	G
Secondary structure
SS confidence
Disorder																												?	?	?	?																?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	A	L	I	I	M	P	V	A	T	R	M	V	V	D	N	A	T	V	L	A	N	Y	F	A	I	S	E	L	T	M	G	L	T	A	I	A	I	G	T	S	L	P	E	L	A	T	A	I	A	G	V	R	K	G	E	N	D	I	A
Secondary structure
SS confidence
Disorder																																																							?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	G	N	I	I	G	A	N	I	F	N	I	V	I	V	L	G	L	P	A	L	I	T	P	G	E	I	D	P	L	A	Y	S	R	D	Y	S	V	M	L	L	V	S	I	I	F	A	L	L	C	W	R	R	S	P	Q	P	G	R	G
Secondary structure
SS confidence
Disorder																								?				?																									?	?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.
Sequence		V	G	V	L	L	T	G	G	F	I	V	W	L	A	M	L	Y	W	L	S	P	I	L	V	E
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 2gfp chain A Region: 5 - 219 Aligned: 215 Modelled: 215 Confidence: 60.0% Identity: 8% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 2knc chain A Region: 129 - 162 Aligned: 34 Modelled: 34 Confidence: 13.4% Identity: 12% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2oar chain A domain 1 Region: 232 - 252 Aligned: 21 Modelled: 21 Confidence: 11.7% Identity: 29% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 3lr6 chain A Region: 19 - 57 Aligned: 39 Modelled: 39 Confidence: 10.0% Identity: 18% PDB header:structural protein Chain: A: PDB Molecule:major ampullate spidroin 1; PDBTitle: self-assembly of spider silk proteins is controlled by a ph-sensitive2 relay Phyre2 PDB 3rko chain M Region: 126 - 204 Aligned: 78 Modelled: 79 Confidence: 9.8% Identity: 12% 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 1wgl chain A Region: 223 - 246 Aligned: 24 Modelled: 24 Confidence: 7.3% Identity: 17% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: CUE domain Phyre2 PDB 3mk7 chain F Region: 124 - 193 Aligned: 70 Modelled: 70 Confidence: 5.9% Identity: 16% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 1dwk chain A domain 1 Region: 27 - 62 Aligned: 36 Modelled: 36 Confidence: 5.6% Identity: 8% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Cyanase N-terminal domain Phyre2 1 c2gfpA_ 2 c2kncA_ 3 d2oara1 4 c3lr6A_ 5 c3rkoM_ 6 d1wgla_ 7 c3mk7F_ 8 d1dwka1

Detailed template information

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

1 c2gfpA_ 60.0 8 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 2 c2kncA_ 13.4 12 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 3 d2oara1 11.7 29 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 4 c3lr6A_ 10.0 18 PDB header:structural protein Chain: A: PDB Molecule:major ampullate spidroin 1; PDBTitle: self-assembly of spider silk proteins is controlled by a ph-sensitive2 relay 5 c3rkoM_ 9.8 12 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 6 d1wgla_ 7.3 17 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:CUE domain 7 c3mk7F_ 5.9 16 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 8 d1dwka1 5.6 8 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Cyanase N-terminal domain

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