Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	A	G	K	S	N	P	L	A	I	S	G	L	V	V	L	T	L	I	W	S	Y	S	W	I	F	M	K	Q	V	T	S	Y	I	G	A	F	D	F	T	A	L	R	C	I	F	G	A	L	V	L	F	I	V	L	L	L	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	R	G	M	R	P	T	P	F	K	Y	T	L	A	I	A	L	L	Q	T	C	G	M	V	G	L	A	Q	W	A	L	V	S	G	G	A	G	K	V	A	I	L	S	Y	T	M	P	F	W	V	V	I	F	A	A	L	F	L	G	E
Secondary structure
SS confidence
Disorder		?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	L	R	R	G	Q	Y	F	A	I	L	I	A	A	F	G	L	F	L	V	L	Q	P	W	Q	L	D	F	S	S	M	K	S	A	M	L	A	I	L	S	G	V	S	W	G	A	S	A	I	V	A	K	R	L	Y	A	R	H	P	R
Secondary structure
SS confidence
Disorder																									?		?	?	?	?																											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	D	L	L	S	L	T	S	W	Q	M	L	Y	A	A	L	V	M	S	V	V	A	L	L	V	P	Q	R	E	I	D	W	Q	P	T	V	F	W	A	L	A	Y	S	A	I	L	A	T	A	L	A	W	S	L	W	L	F	V	L	K
Secondary structure
SS confidence
Disorder		?																							?		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		N	L	P	A	S	I	A	S	L	S	T	L	A	V	P	V	C	G	V	L	F	S	W	W	L	L	G	E	N	P	G	A	V	E	G	S	G	I	V	L	I	V	L	A	L	A	L	V	S	R	K	K	K	E	A	V	S	V	K	R
Secondary structure
SS confidence
Disorder																																																		?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.
Sequence		I
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 1s7b chain A Region: 223 - 297 Aligned: 75 Modelled: 75 Confidence: 97.7% Identity: 19% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 2i68 chain B Region: 227 - 290 Aligned: 58 Modelled: 64 Confidence: 91.5% Identity: 21% PDB header:transport protein Chain: B: PDB Molecule:protein emre; PDBTitle: cryo-em based theoretical model structure of transmembrane2 domain of the multidrug-resistance antiporter from e. coli3 emre Phyre2 PDB 3rko chain F Region: 159 - 298 Aligned: 138 Modelled: 140 Confidence: 68.7% Identity: 17% PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2b2h chain A Region: 4 - 243 Aligned: 238 Modelled: 240 Confidence: 40.2% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 2l2t chain A Region: 278 - 300 Aligned: 23 Modelled: 23 Confidence: 20.2% Identity: 17% 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 3b9y chain A Region: 4 - 243 Aligned: 229 Modelled: 240 Confidence: 15.8% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 2jp3 chain A Region: 275 - 300 Aligned: 26 Modelled: 26 Confidence: 10.7% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles Phyre2 PDB 1u7g chain A Region: 11 - 243 Aligned: 232 Modelled: 233 Confidence: 9.6% Identity: 8% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 2jo1 chain A Region: 275 - 300 Aligned: 26 Modelled: 26 Confidence: 7.0% Identity: 12% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 3aqp chain B Region: 214 - 300 Aligned: 87 Modelled: 87 Confidence: 5.7% Identity: 17% PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus Phyre2 1 d1s7ba_ 2 c2i68B_ 3 c3rkoF_ 4 c2b2hA_ 5 c2l2tA_ 6 c3b9yA_ 7 c2jp3A_ 8 d1u7ga_ 9 c2jo1A_ 10 c3aqpB_

Detailed template information

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

1 d1s7ba_ 97.7 19 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 c2i68B_ 91.5 21 PDB header:transport protein Chain: B: PDB Molecule:protein emre; PDBTitle: cryo-em based theoretical model structure of transmembrane2 domain of the multidrug-resistance antiporter from e. coli3 emre 3 c3rkoF_ 68.7 17 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 4 c2b2hA_ 40.2 11 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 5 c2l2tA_ 20.2 17 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 6 c3b9yA_ 15.8 10 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 7 c2jp3A_ 10.7 19 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 8 d1u7ga_ 9.6 8 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 9 c2jo1A_ 7.0 12 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 10 c3aqpB_ 5.7 17 PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus

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