Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	H	V	W	G	L	F	S	H	P	D	R	E	M	Q	V	I	N	R	E	N	E	T	I	S	H	H	Y	T	H	H	V	L	L	M	A	A	I	P	V	I	C	A	F	I	G	T	T	Q	I	G	W	N	F	G	D	G	T	I
Secondary structure
SS confidence
Disorder		?	?																?	?	?	?	?	?																																			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	K	L	S	W	F	T	G	L	A	L	A	V	L	F	Y	G	V	M	L	A	G	V	A	V	M	G	R	V	I	W	W	M	A	R	N	Y	P	Q	R	P	S	L	A	H	C	M	V	F	A	G	Y	V	A	T	P	L	F	L	S
Secondary structure
SS confidence
Disorder		?	?	?		?	?																																?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	L	V	A	L	Y	P	L	V	W	L	C	A	L	V	G	T	V	A	L	F	Y	T	G	Y	L	L	Y	L	G	I	P	S	F	L	N	I	N	K	E	E	G	L	S	F	S	S	S	T	L	A	I	G	V	L	V	L	E	V	L
Secondary structure
SS confidence
Disorder																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.
Sequence		L	A	L	T	V	I	L	W	G	Y	G	Y	R	L	F
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 1kf6 chain C Region: 127 - 180 Aligned: 54 Modelled: 54 Confidence: 22.2% Identity: 19% 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 3ddl chain B Region: 19 - 179 Aligned: 158 Modelled: 161 Confidence: 19.0% Identity: 10% PDB header:transport protein Chain: B: PDB Molecule:xanthorhodopsin; PDBTitle: crystallographic structure of xanthorhodopsin, a light-2 driven ion pump with dual chromophore Phyre2 PDB 1h2s chain A Region: 19 - 175 Aligned: 143 Modelled: 157 Confidence: 16.5% Identity: 11% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 3a7k chain D Region: 19 - 174 Aligned: 151 Modelled: 156 Confidence: 11.3% Identity: 9% PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis Phyre2 PDB 3rko chain N Region: 13 - 134 Aligned: 114 Modelled: 122 Confidence: 11.2% Identity: 17% 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 3rko chain M Region: 9 - 146 Aligned: 126 Modelled: 138 Confidence: 10.7% 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 2vay chain B Region: 141 - 161 Aligned: 21 Modelled: 20 Confidence: 10.7% Identity: 24% PDB header:metal transport Chain: B: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: calmodulin complexed with cav1.1 iq peptide Phyre2 PDB 1pw4 chain A Region: 9 - 193 Aligned: 181 Modelled: 185 Confidence: 10.4% Identity: 11% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1eys chain H domain 2 Region: 140 - 161 Aligned: 22 Modelled: 22 Confidence: 8.1% Identity: 14% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 2knc chain A Region: 168 - 192 Aligned: 25 Modelled: 25 Confidence: 7.9% Identity: 24% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2kb1 chain A Region: 54 - 106 Aligned: 49 Modelled: 53 Confidence: 7.5% Identity: 20% PDB header:membrane protein Chain: A: PDB Molecule:wsk3; PDBTitle: nmr studies of a channel protein without membrane:2 structure and dynamics of water-solubilized kcsa Phyre2 PDB 2axt chain Z domain 1 Region: 135 - 186 Aligned: 52 Modelled: 52 Confidence: 6.5% Identity: 21% Fold: Transmembrane helix hairpin Superfamily: PsbZ-like Family: PsbZ-like Phyre2 PDB 2jag chain A Region: 19 - 174 Aligned: 151 Modelled: 156 Confidence: 5.9% Identity: 6% PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v Phyre2 PDB 2k1h chain A Region: 10 - 21 Aligned: 12 Modelled: 12 Confidence: 5.8% Identity: 0% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ser13; PDBTitle: solution nmr structure of ser13 from staphylococcus epidermidis.2 northeast structural genomics consortium target ser13 Phyre2 PDB 2xq2 chain A Region: 10 - 182 Aligned: 173 Modelled: 173 Confidence: 5.5% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 1 d1kf6c_ 2 c3ddlB_ 3 d1h2sa_ 4 c3a7kD_ 5 c3rkoN_ 6 c3rkoM_ 7 c2vayB_ 8 d1pw4a_ 9 d1eysh2 10 c2kncA_ 11 c2kb1A_ 12 d2axtz1 13 c2jagA_ 14 c2k1hA_ 15 c2xq2A_

Detailed template information

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

1 d1kf6c_ 22.2 19 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) 2 c3ddlB_ 19.0 10 PDB header:transport protein Chain: B: PDB Molecule:xanthorhodopsin; PDBTitle: crystallographic structure of xanthorhodopsin, a light-2 driven ion pump with dual chromophore 3 d1h2sa_ 16.5 11 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 4 c3a7kD_ 11.3 9 PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis 5 c3rkoN_ 11.2 17 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 c3rkoM_ 10.7 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 7 c2vayB_ 10.7 24 PDB header:metal transport Chain: B: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: calmodulin complexed with cav1.1 iq peptide 8 d1pw4a_ 10.4 11 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 9 d1eysh2 8.1 14 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 10 c2kncA_ 7.9 24 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 11 c2kb1A_ 7.5 20 PDB header:membrane protein Chain: A: PDB Molecule:wsk3; PDBTitle: nmr studies of a channel protein without membrane:2 structure and dynamics of water-solubilized kcsa 12 d2axtz1 6.5 21 Fold:Transmembrane helix hairpin Superfamily:PsbZ-like Family:PsbZ-like 13 c2jagA_ 5.9 6 PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v 14 c2k1hA_ 5.8 0 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ser13; PDBTitle: solution nmr structure of ser13 from staphylococcus epidermidis.2 northeast structural genomics consortium target ser13 15 c2xq2A_ 5.5 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt

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