Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	S	S	Y	L	H	F	P	E	F	D	P	V	I	F	S	I	G	P	V	A	L	H	W	Y	G	L	M	Y	L	V	G	F	I	F	A	M	W	L	A	T	R	R	A	N	R	P	G	S	G	W	T	K	N	E	V	E	N	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																								?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	Y	A	G	F	L	G	V	F	L	G	G	R	I	G	Y	V	L	F	Y	N	F	P	Q	F	M	A	D	P	L	Y	L	F	R	V	W	D	G	G	M	S	F	H	G	G	L	I	G	V	I	V	V	M	I	I	F	A	R	R	T
Secondary structure
SS confidence
Disorder																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	R	S	F	F	Q	V	S	D	F	I	A	P	L	I	P	F	G	L	G	A	G	R	L	G	N	F	I	N	G	E	L	W	G	R	V	D	P	N	F	P	F	A	M	L	F	P	G	S	R	T	E	D	I	L	L	L	Q	T	N
Secondary structure
SS confidence
Disorder																																																				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	Q	W	Q	S	I	F	D	T	Y	G	V	L	P	R	H	P	S	Q	L	Y	E	L	L	L	E	G	V	V	L	F	I	I	L	N	L	Y	I	R	K	P	R	P	M	G	A	V	S	G	L	F	L	I	G	Y	G	A	F	R	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.
Sequence		I	V	E	F	F	R	Q	P	D	A	Q	F	T	G	A	W	V	Q	Y	I	S	M	G	Q	I	L	S	I	P	M	I	V	A	G	V	I	M	M	V	W	A	Y	R	R	S	P	Q	Q	H	V	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 2i5n chain L domain 1 Region: 12 - 45 Aligned: 34 Modelled: 34 Confidence: 14.0% Identity: 21% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 PDB 2k9y chain B Region: 266 - 284 Aligned: 19 Modelled: 19 Confidence: 11.3% Identity: 21% PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 2j8c chain L domain 1 Region: 11 - 45 Aligned: 35 Modelled: 35 Confidence: 9.6% Identity: 17% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 PDB 2k9y chain A Region: 266 - 284 Aligned: 19 Modelled: 19 Confidence: 9.1% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 1eys chain H domain 2 Region: 260 - 288 Aligned: 29 Modelled: 29 Confidence: 7.8% 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 1s7b chain A Region: 203 - 287 Aligned: 75 Modelled: 84 Confidence: 6.8% Identity: 15% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 3lrc chain C Region: 204 - 289 Aligned: 74 Modelled: 86 Confidence: 6.5% Identity: 14% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 3rko chain K Region: 197 - 291 Aligned: 91 Modelled: 92 Confidence: 5.8% Identity: 15% PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 1k6n chain H Region: 23 - 55 Aligned: 31 Modelled: 33 Confidence: 5.5% Identity: 13% PDB header:photosynthesis Chain: H: PDB Molecule:photosynthetic reaction center h subunit; PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides Phyre2 1 d2i5nl1 2 c2k9yB_ 3 d2j8cl1 4 c2k9yA_ 5 d1eysh2 6 d1s7ba_ 7 c3lrcC_ 8 c3rkoK_ 9 c1k6nH_

Detailed template information

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

1 d2i5nl1 14.0 21 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits 2 c2k9yB_ 11.3 21 PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 3 d2j8cl1 9.6 17 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits 4 c2k9yA_ 9.1 21 PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 5 d1eysh2 7.8 14 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 6 d1s7ba_ 6.8 15 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 7 c3lrcC_ 6.5 14 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 8 c3rkoK_ 5.8 15 PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 9 c1k6nH_ 5.5 13 PDB header:photosynthesis Chain: H: PDB Molecule:photosynthetic reaction center h subunit; PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides

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