Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	F	R	Q	L	L	P	L	F	G	A	L	F	A	L	Y	I	I	W	G	S	T	Y	F	V	I	R	I	G	V	E	S	W	P	P	L	M	M	A	G	V	R	F	L	A	A	G	I	L	L	L	A	F	L	L	L	R	G	H
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																																				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	L	P	P	L	R	P	L	L	N	A	A	L	I	G	L	L	L	L	A	V	G	N	G	M	V	T	V	A	E	H	Q	N	V	P	S	G	I	A	A	V	V	V	A	T	V	P	L	F	T	L	C	F	S	R	L	F	G	I	K
Secondary structure
SS confidence
Disorder		?	?	?	?																													?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	R	K	L	E	W	V	G	I	A	I	G	L	A	G	I	I	M	L	N	S	G	G	N	L	S	G	N	P	W	G	A	I	L	I	L	I	G	S	I	S	W	A	F	G	S	V	Y	G	S	R	I	T	L	P	V	G	M	M	A
Secondary structure
SS confidence
Disorder																								?	?	?	?	?																								?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	A	I	E	M	L	A	A	G	V	V	L	M	I	A	S	M	I	A	G	E	K	L	T	A	L	P	S	L	S	G	F	L	A	V	G	Y	L	A	L	F	G	S	I	I	A	I	N	A	Y	M	Y	L	I	R	N	V	S	P	A
Secondary structure
SS confidence
Disorder																						?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	A	T	S	Y	A	Y	V	N	P	V	V	A	V	L	L	G	T	G	L	G	G	E	T	L	S	K	I	E	W	L	A	L	G	V	I	V	F	A	V	V	L	V	T	L	G	K	Y	L	F	P	A	K	P	V	V	A	P	V	I
Secondary structure
SS confidence
Disorder																																														?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.
Sequence		Q	D	A	S	S	E
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: 218 - 292 Aligned: 75 Modelled: 75 Confidence: 97.4% Identity: 16% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 2i68 chain B Region: 222 - 285 Aligned: 58 Modelled: 64 Confidence: 91.1% Identity: 24% 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 2xq2 chain A Region: 155 - 302 Aligned: 148 Modelled: 148 Confidence: 74.0% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 PDB 1u7g chain A Region: 6 - 238 Aligned: 230 Modelled: 233 Confidence: 68.1% Identity: 15% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 3dh4 chain A Region: 155 - 305 Aligned: 151 Modelled: 151 Confidence: 60.4% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus Phyre2 PDB 2jp3 chain A Region: 270 - 303 Aligned: 34 Modelled: 34 Confidence: 57.3% Identity: 9% 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 3rko chain F Region: 8 - 149 Aligned: 142 Modelled: 142 Confidence: 38.9% Identity: 10% 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 3lrc chain C Region: 183 - 294 Aligned: 112 Modelled: 112 Confidence: 36.4% Identity: 12% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 1iwg chain A domain 8 Region: 215 - 306 Aligned: 92 Modelled: 92 Confidence: 32.1% Identity: 13% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 2jln chain A Region: 248 - 306 Aligned: 59 Modelled: 59 Confidence: 17.6% Identity: 5% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 1iwg chain A domain 7 Region: 215 - 306 Aligned: 92 Modelled: 92 Confidence: 17.0% Identity: 10% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1oy8 chain A Region: 215 - 306 Aligned: 92 Modelled: 92 Confidence: 16.9% Identity: 9% PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump Phyre2 PDB 2knc chain A Region: 273 - 306 Aligned: 34 Modelled: 34 Confidence: 16.2% Identity: 15% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3aqp chain B Region: 210 - 301 Aligned: 92 Modelled: 92 Confidence: 16.2% Identity: 16% 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 PDB 2jo1 chain A Region: 270 - 305 Aligned: 36 Modelled: 36 Confidence: 13.7% Identity: 8% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 3dtu chain B domain 2 Region: 270 - 306 Aligned: 37 Modelled: 37 Confidence: 11.5% Identity: 16% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3ehb chain B domain 2 Region: 270 - 306 Aligned: 37 Modelled: 37 Confidence: 10.5% Identity: 22% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1fft chain B domain 2 Region: 275 - 305 Aligned: 31 Modelled: 31 Confidence: 9.0% Identity: 13% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3gia chain A Region: 59 - 303 Aligned: 224 Modelled: 245 Confidence: 6.3% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 2b2h chain A Region: 6 - 238 Aligned: 232 Modelled: 233 Confidence: 6.0% Identity: 14% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 1 d1s7ba_ 2 c2i68B_ 3 c2xq2A_ 4 d1u7ga_ 5 c3dh4A_ 6 c2jp3A_ 7 c3rkoF_ 8 c3lrcC_ 9 d1iwga8 10 c2jlnA_ 11 d1iwga7 12 c1oy8A_ 13 c2kncA_ 14 c3aqpB_ 15 c2jo1A_ 16 d3dtub2 17 d3ehbb2 18 d1fftb2 19 c3giaA_ 20 c2b2hA_ 21 22

Detailed template information

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

1 d1s7ba_ 97.4 16 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 c2i68B_ 91.1 24 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 c2xq2A_ 74.0 12 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 4 d1u7ga_ 68.1 15 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 5 c3dh4A_ 60.4 12 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 6 c2jp3A_ 57.3 9 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 7 c3rkoF_ 38.9 10 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 8 c3lrcC_ 36.4 12 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 9 d1iwga8 32.1 13 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 10 c2jlnA_ 17.6 5 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 11 d1iwga7 17.0 10 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 12 c1oy8A_ 16.9 9 PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump 13 c2kncA_ 16.2 15 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 14 c3aqpB_ 16.2 16 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 15 c2jo1A_ 13.7 8 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 16 d3dtub2 11.5 16 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 17 d3ehbb2 10.5 22 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 18 d1fftb2 9.0 13 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 19 c3giaA_ 6.3 12 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 20 c2b2hA_ 6.0 14 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 21 c2mltB_ not modelled 5.2 12 PDB header:toxin (hemolytic polypeptide) Chain: B: PDB Molecule:melittin; PDBTitle: melittin 22 c2mltA_ not modelled 5.2 12 PDB header:toxin (hemolytic polypeptide) Chain: A: PDB Molecule:melittin; PDBTitle: melittin

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