Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	A	L	L	E	H	F	I	T	Q	S	T	V	Y	S	L	M	A	V	V	L	V	A	F	L	E	S	L	A	L	V	G	L	I	L	P	G	T	V	L	M	A	G	L	G	A	L	I	G	S	G	E	L	S	F	W	H	A	W
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	A	G	I	I	G	C	L	M	G	D	W	I	S	F	W	L	G	W	R	F	K	K	P	L	H	R	W	S	F	L	K	K	N	K	A	L	L	D	K	T	E	H	A	L	H	Q	H	S	M	F	T	I	L	V	G	R	F	V	G
Secondary structure
SS confidence
Disorder																																	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	T	R	P	L	V	P	M	V	A	G	M	L	D	L	P	V	A	K	F	I	T	P	N	I	I	G	C	L	L	W	P	P	F	Y	F	L	P	G	I	L	A	G	A	A	I	D	I	P	A	G	M	Q	S	G	E	F	K	W	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	L	A	T	A	V	F	L	W	V	G	G	W	L	C	W	R	L	W	R	S	G	K	A	T	D	R	L	S	H	Y	L	S	R	G	R	L	L	W	L	T	P	L	I	S	A	I	G	V	V	A	L	V	V	L	I	R	H	P	L
Secondary structure
SS confidence
Disorder																						?	?	?	?	?	?	?					?	?						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.
Sequence		M	P	V	Y	I	D	I	L	R	K	V	V	G	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 3ehb chain B domain 2 Region: 163 - 219 Aligned: 57 Modelled: 57 Confidence: 16.9% Identity: 7% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1fft chain B domain 2 Region: 163 - 206 Aligned: 44 Modelled: 44 Confidence: 14.9% 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 1ar1 chain B Region: 163 - 219 Aligned: 57 Modelled: 57 Confidence: 14.3% Identity: 7% PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment Phyre2 PDB 1qle chain B Region: 163 - 219 Aligned: 57 Modelled: 57 Confidence: 14.3% Identity: 7% PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment Phyre2 PDB 2oso chain A domain 1 Region: 71 - 110 Aligned: 32 Modelled: 37 Confidence: 12.4% Identity: 16% Fold: Ligand-binding domain in the NO signalling and Golgi transport Superfamily: Ligand-binding domain in the NO signalling and Golgi transport Family: MJ1460-like Phyre2 PDB 2lbg chain A Region: 62 - 78 Aligned: 17 Modelled: 17 Confidence: 10.9% Identity: 29% PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles Phyre2 PDB 1fft chain G Region: 163 - 234 Aligned: 72 Modelled: 72 Confidence: 9.6% Identity: 11% PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli Phyre2 PDB 3dtu chain B domain 2 Region: 163 - 219 Aligned: 57 Modelled: 57 Confidence: 9.3% Identity: 9% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2bbj chain B Region: 95 - 198 Aligned: 70 Modelled: 70 Confidence: 8.8% 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 1p58 chain F Region: 96 - 116 Aligned: 21 Modelled: 21 Confidence: 8.4% Identity: 24% PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction Phyre2 PDB 2csb chain A domain 4 Region: 99 - 112 Aligned: 14 Modelled: 14 Confidence: 7.7% Identity: 14% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Topoisomerase V repeat domain Phyre2 PDB 2l9u chain A Region: 54 - 80 Aligned: 27 Modelled: 27 Confidence: 6.3% Identity: 19% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain Phyre2 PDB 1w6k chain A domain 2 Region: 31 - 112 Aligned: 74 Modelled: 82 Confidence: 6.1% Identity: 9% Fold: alpha/alpha toroid Superfamily: Terpenoid cyclases/Protein prenyltransferases Family: Terpene synthases Phyre2 PDB 1y5i chain C domain 1 Region: 151 - 209 Aligned: 59 Modelled: 59 Confidence: 5.9% Identity: 14% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 2hn8 chain A Region: 191 - 217 Aligned: 27 Modelled: 27 Confidence: 5.7% Identity: 26% PDB header:viral protein Chain: A: PDB Molecule:protein pb1-f2; PDBTitle: structural characterization and oligomerization of pb1-f2,2 a pro-apoptotic influenza a virus protein Phyre2 1 d3ehbb2 2 d1fftb2 3 c1ar1B_ 4 c1qleB_ 5 d2osoa1 6 c2lbgA_ 7 c1fftG_ 8 d3dtub2 9 c2bbjB_ 10 c1p58F_ 11 d2csba4 12 c2l9uA_ 13 d1w6ka2 14 d1y5ic1 15 c2hn8A_

Detailed template information

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

1 d3ehbb2 16.9 7 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 2 d1fftb2 14.9 14 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 3 c1ar1B_ 14.3 7 PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment 4 c1qleB_ 14.3 7 PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment 5 d2osoa1 12.4 16 Fold:Ligand-binding domain in the NO signalling and Golgi transport Superfamily:Ligand-binding domain in the NO signalling and Golgi transport Family:MJ1460-like 6 c2lbgA_ 10.9 29 PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles 7 c1fftG_ 9.6 11 PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli 8 d3dtub2 9.3 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 9 c2bbjB_ 8.8 16 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 10 c1p58F_ 8.4 24 PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 11 d2csba4 7.7 14 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Topoisomerase V repeat domain 12 c2l9uA_ 6.3 19 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain 13 d1w6ka2 6.1 9 Fold:alpha/alpha toroid Superfamily:Terpenoid cyclases/Protein prenyltransferases Family:Terpene synthases 14 d1y5ic1 5.9 14 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 15 c2hn8A_ 5.7 26 PDB header:viral protein Chain: A: PDB Molecule:protein pb1-f2; PDBTitle: structural characterization and oligomerization of pb1-f2,2 a pro-apoptotic influenza a virus protein

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