Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	L	I	Y	F	L	I	D	F	I	L	H	I	D	V	H	L	A	E	L	V	A	E	Y	G	V	W	V	Y	A	I	L	F	L	I	L	F	C	E	T	G	L	V	V	T	P	F	L	P	G	D	S	L	L	F	V	A	G	A
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	A	S	L	E	T	N	D	L	N	V	H	M	M	V	V	L	M	L	I	A	A	I	V	G	D	A	V	N	Y	T	I	G	R	L	F	G	E	K	L	F	S	N	P	N	S	K	I	F	R	R	S	Y	L	D	K	T	H	Q	F
Secondary structure
SS confidence
Disorder																																															?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	E	K	H	G	G	K	T	I	I	L	A	R	F	V	P	I	V	R	T	F	A	P	F	V	A	G	M	G	H	M	S	Y	R	H	F	A	A	Y	N	V	I	G	A	L	L	W	V	L	L	F	T	Y	A	G	Y	F	F	G	T
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.
Sequence		I	P	M	V	Q	D	N	L	K	L	L	I	V	G	I	I	V	V	S	I	L	P	G	V	I	E	I	I	R	H	K	R	A	A	A	R	A	A	K
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 2bbj chain B Region: 114 - 212 Aligned: 67 Modelled: 67 Confidence: 57.6% Identity: 19% 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 2vv5 chain A domain 3 Region: 78 - 148 Aligned: 70 Modelled: 71 Confidence: 15.9% Identity: 14% Fold: Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily: Mechanosensitive channel protein MscS (YggB), transmembrane region Family: Mechanosensitive channel protein MscS (YggB), transmembrane region Phyre2 PDB 3p5n chain A Region: 50 - 88 Aligned: 32 Modelled: 39 Confidence: 10.1% Identity: 13% 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 2l2t chain A Region: 190 - 217 Aligned: 28 Modelled: 28 Confidence: 9.4% Identity: 21% 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 1fft chain B domain 2 Region: 178 - 219 Aligned: 42 Modelled: 42 Confidence: 8.3% Identity: 12% 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: 175 - 219 Aligned: 45 Modelled: 45 Confidence: 6.7% Identity: 11% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2klu chain A Region: 187 - 219 Aligned: 33 Modelled: 33 Confidence: 6.2% Identity: 18% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 3gia chain A Region: 31 - 216 Aligned: 186 Modelled: 186 Confidence: 6.1% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 2oso chain A domain 1 Region: 86 - 126 Aligned: 32 Modelled: 38 Confidence: 6.0% Identity: 19% 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 2iub chain A domain 2 Region: 154 - 212 Aligned: 44 Modelled: 45 Confidence: 5.9% Identity: 16% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 3ehb chain B domain 2 Region: 180 - 219 Aligned: 40 Modelled: 40 Confidence: 5.9% Identity: 18% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1f16 chain A Region: 2 - 34 Aligned: 33 Modelled: 33 Confidence: 5.4% Identity: 18% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1qle chain B Region: 175 - 219 Aligned: 45 Modelled: 45 Confidence: 5.2% Identity: 16% 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 1 c2bbjB_ 2 d2vv5a3 3 c3p5nA_ 4 c2l2tA_ 5 d1fftb2 6 d3dtub2 7 c2kluA_ 8 c3giaA_ 9 d2osoa1 10 d2iuba2 11 d3ehbb2 12 d1f16a_ 13 c1qleB_

Detailed template information

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

1 c2bbjB_ 57.6 19 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 2 d2vv5a3 15.9 14 Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region Family:Mechanosensitive channel protein MscS (YggB), transmembrane region 3 c3p5nA_ 10.1 13 PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter 4 c2l2tA_ 9.4 21 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 5 d1fftb2 8.3 12 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 6 d3dtub2 6.7 11 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 7 c2kluA_ 6.2 18 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 8 c3giaA_ 6.1 12 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 9 d2osoa1 6.0 19 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 10 d2iuba2 5.9 16 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 11 d3ehbb2 5.9 18 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 12 d1f16a_ 5.4 18 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 13 c1qleB_ 5.2 16 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

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