Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	L	T	A	K	Q	V	T	W	L	K	V	C	L	H	L	A	G	L	L	P	F	L	W	L	V	W	A	I	N	H	G	G	L	G	A	D	P	V	K	D	I	Q	H	F	T	G	R	T	A	L	K	F	L	L	A	T	L	L
Secondary structure
SS confidence
Disorder		?	?	?	?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	T	P	L	A	R	Y	A	K	Q	P	L	L	I	R	T	R	R	L	L	G	L	W	C	F	A	W	A	T	L	H	L	T	S	Y	A	L	L	E	L	G	V	N	N	L	A	L	L	G	K	E	L	I	T	R	P	Y	L	T	L
Secondary structure
SS confidence
Disorder		?							?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	I	I	S	W	V	I	L	L	A	L	A	F	T	S	T	Q	A	M	Q	R	K	L	G	K	H	W	Q	Q	L	H	N	F	V	Y	L	V	A	I	L	A	P	I	H	Y	L	W	S	V	K	I	I	S	P	Q	P	L	I	Y	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.
Sequence		G	L	A	V	L	L	L	A	L	R	Y	K	K	L	R	S	L	F	N	R	L	R	K	Q	V	H	N	K	L	S	V
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 1m0k chain A Region: 113 - 166 Aligned: 54 Modelled: 54 Confidence: 14.7% Identity: 13% PDB header:ion transport Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: bacteriorhodopsin k intermediate at 1.43 a resolution Phyre2 PDB 1m0k chain A Region: 113 - 166 Aligned: 54 Modelled: 54 Confidence: 14.7% Identity: 13% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 1q90 chain B Region: 73 - 176 Aligned: 95 Modelled: 104 Confidence: 9.9% Identity: 19% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1nek chain C Region: 75 - 140 Aligned: 63 Modelled: 66 Confidence: 9.3% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1jb0 chain B Region: 73 - 130 Aligned: 58 Modelled: 58 Confidence: 9.0% Identity: 14% Fold: Photosystem I subunits PsaA/PsaB Superfamily: Photosystem I subunits PsaA/PsaB Family: Photosystem I subunits PsaA/PsaB Phyre2 PDB 1jb0 chain A Region: 73 - 130 Aligned: 58 Modelled: 58 Confidence: 7.6% Identity: 10% Fold: Photosystem I subunits PsaA/PsaB Superfamily: Photosystem I subunits PsaA/PsaB Family: Photosystem I subunits PsaA/PsaB Phyre2 PDB 2kix chain D Region: 78 - 97 Aligned: 20 Modelled: 20 Confidence: 7.5% Identity: 20% PDB header:transport protein Chain: D: PDB Molecule:bm2 protein; PDBTitle: channel domain of bm2 protein from influenza b virus Phyre2 PDB 2e74 chain A domain 1 Region: 73 - 176 Aligned: 95 Modelled: 104 Confidence: 6.8% Identity: 19% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1c8s chain A Region: 113 - 166 Aligned: 54 Modelled: 54 Confidence: 6.6% Identity: 13% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 1xme chain C domain 1 Region: 79 - 88 Aligned: 10 Modelled: 10 Confidence: 6.2% Identity: 30% Fold: Single transmembrane helix Superfamily: Bacterial ba3 type cytochrome c oxidase subunit IIa Family: Bacterial ba3 type cytochrome c oxidase subunit IIa Phyre2 PDB 1yq3 chain C Region: 75 - 163 Aligned: 88 Modelled: 89 Confidence: 5.9% Identity: 13% PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone Phyre2 PDB 1v54 chain M Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 5.5% Identity: 20% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Phyre2 PDB 2ks1 chain B Region: 114 - 142 Aligned: 29 Modelled: 29 Confidence: 5.5% Identity: 17% PDB header:transferase Chain: B: PDB Molecule:epidermal growth factor receptor; PDBTitle: heterodimeric association of transmembrane domains of erbb1 and erbb22 receptors enabling kinase activation Phyre2 PDB 2l2t chain A Region: 114 - 142 Aligned: 29 Modelled: 29 Confidence: 5.3% Identity: 17% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain Phyre2 PDB 3gia chain A Region: 118 - 208 Aligned: 91 Modelled: 91 Confidence: 5.3% Identity: 5% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 2y69 chain Z Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 5.2% Identity: 20% PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 1 c1m0kA_ 2 d1m0ka_ 3 d1q90b_ 4 d1nekc_ 5 d1jb0b_ 6 d1jb0a_ 7 c2kixD_ 8 d2e74a1 9 d1c8sa_ 10 d1xmec1 11 c1yq3C_ 12 d1v54m_ 13 c2ks1B_ 14 c2l2tA_ 15 c3giaA_ 16 c2y69Z_

Detailed template information

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

1 c1m0kA_ 14.7 13 PDB header:ion transport Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: bacteriorhodopsin k intermediate at 1.43 a resolution 2 d1m0ka_ 14.7 13 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 3 d1q90b_ 9.9 19 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 4 d1nekc_ 9.3 17 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 5 d1jb0b_ 9.0 14 Fold:Photosystem I subunits PsaA/PsaB Superfamily:Photosystem I subunits PsaA/PsaB Family:Photosystem I subunits PsaA/PsaB 6 d1jb0a_ 7.6 10 Fold:Photosystem I subunits PsaA/PsaB Superfamily:Photosystem I subunits PsaA/PsaB Family:Photosystem I subunits PsaA/PsaB 7 c2kixD_ 7.5 20 PDB header:transport protein Chain: D: PDB Molecule:bm2 protein; PDBTitle: channel domain of bm2 protein from influenza b virus 8 d2e74a1 6.8 19 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 d1c8sa_ 6.6 13 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 10 d1xmec1 6.2 30 Fold:Single transmembrane helix Superfamily:Bacterial ba3 type cytochrome c oxidase subunit IIa Family:Bacterial ba3 type cytochrome c oxidase subunit IIa 11 c1yq3C_ 5.9 13 PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone 12 d1v54m_ 5.5 20 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) 13 c2ks1B_ 5.5 17 PDB header:transferase Chain: B: PDB Molecule:epidermal growth factor receptor; PDBTitle: heterodimeric association of transmembrane domains of erbb1 and erbb22 receptors enabling kinase activation 14 c2l2tA_ 5.3 17 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 15 c3giaA_ 5.3 5 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 16 c2y69Z_ 5.2 20 PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen

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