Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	S	G	W	H	E	W	P	L	M	I	F	T	V	F	G	Q	C	V	A	G	G	F	I	V	L	A	L	A	L	L	K	G	D	L	R	A	E	A	Q	Q	R	V	I	A	C	M	F	G	L	W	V	L	M	G	I	G	F	I
Secondary structure
SS confidence
Disorder		?	?	?	?																													?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	S	M	L	H	L	G	S	P	M	R	A	F	N	S	L	N	R	V	G	A	S	A	L	S	N	E	I	A	S	G	S	I	F	F	A	V	G	G	I	G	W	L	L	A	M	L	K	K	L	S	P	A	L	R	T	L	W	L	I
Secondary structure
SS confidence
Disorder																				?	?	?	?																											?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	T	M	V	L	G	V	I	F	V	W	M	M	V	R	V	Y	N	S	I	D	T	V	P	T	W	Y	S	I	W	T	P	M	G	F	F	L	T	M	F	M	G	G	P	L	L	G	Y	L	L	L	S	L	A	G	V	D	G	W	A
Secondary structure
SS confidence
Disorder																			?	?	?		?																																	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		M	R	L	L	P	A	I	S	V	L	A	L	V	V	S	G	V	V	S	V	M	Q	G	A	E	L	A	T	I	H	S	S	V	Q	Q	A	A	A	L	V	P	D	Y	G	A	L	M	S	W	R	I	V	L	L	A	V	A	L	C	L
Secondary structure
SS confidence
Disorder																										?	?	?		?	?	?								?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.
Sequence		W	I	A	P	Q	L	K	G	Y	Q	P	A	V	P	L	L	S	V	S	F	I	L	L	L	A	G	E	L	I	G	R	G	V	F	Y	G	L	H	M	T	V	G	M	A	V	A	S
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 2vpz chain G Region: 6 - 273 Aligned: 227 Modelled: 241 Confidence: 100.0% Identity: 19% PDB header:oxidoreductase Chain: G: PDB Molecule:hypothetical membrane spanning protein; PDBTitle: polysulfide reductase native structure Phyre2 PDB 2jag chain A Region: 147 - 279 Aligned: 133 Modelled: 133 Confidence: 56.0% Identity: 12% PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v Phyre2 PDB 1e12 chain A Region: 147 - 279 Aligned: 133 Modelled: 133 Confidence: 38.8% Identity: 12% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 2amn chain A Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 13.6% Identity: 55% PDB header:antimicrobial protein Chain: A: PDB Molecule:cathelicidin; PDBTitle: solution structure of fowlicidin-1, a novel cathelicidin2 antimicrobial peptide from chicken Phyre2 PDB 3rko chain A Region: 13 - 113 Aligned: 93 Modelled: 101 Confidence: 11.1% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:nadh-quinone oxidoreductase subunit a; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2p9x chain B Region: 264 - 287 Aligned: 24 Modelled: 24 Confidence: 6.6% Identity: 17% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3 Phyre2 PDB 2jwa chain A Region: 109 - 143 Aligned: 35 Modelled: 35 Confidence: 6.4% Identity: 17% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 1m56 chain G Region: 5 - 254 Aligned: 238 Modelled: 250 Confidence: 6.2% Identity: 8% PDB header:oxidoreductase Chain: G: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobactor2 sphaeroides (wild type) Phyre2 1 c2vpzG_ 2 c2jagA_ 3 d1e12a_ 4 c2amnA_ 5 c3rkoA_ 6 c2p9xB_ 7 c2jwaA_ 8 c1m56G_

Detailed template information

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

1 c2vpzG_ 100.0 19 PDB header:oxidoreductase Chain: G: PDB Molecule:hypothetical membrane spanning protein; PDBTitle: polysulfide reductase native structure 2 c2jagA_ 56.0 12 PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v 3 d1e12a_ 38.8 12 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 4 c2amnA_ 13.6 55 PDB header:antimicrobial protein Chain: A: PDB Molecule:cathelicidin; PDBTitle: solution structure of fowlicidin-1, a novel cathelicidin2 antimicrobial peptide from chicken 5 c3rkoA_ 11.1 13 PDB header:oxidoreductase Chain: A: PDB Molecule:nadh-quinone oxidoreductase subunit a; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 6 c2p9xB_ 6.6 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3 7 c2jwaA_ 6.4 17 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 8 c1m56G_ 6.2 8 PDB header:oxidoreductase Chain: G: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobactor2 sphaeroides (wild type)

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