Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	S	G	V	L	Y	A	L	L	A	G	L	M	W	G	L	I	F	V	G	P	L	I	V	P	E	Y	P	A	M	L	Q	S	M	G	R	Y	L	A	L	G	L	I	A	L	P	I	A	W	L	G	R	V	R	L	R	Q	L	A
Secondary structure
SS confidence
Disorder		?																																																					?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	R	D	W	L	T	A	L	M	L	T	M	M	G	N	L	I	Y	Y	F	C	L	A	S	A	I	Q	R	T	G	A	P	V	S	T	M	I	I	G	T	L	P	V	V	I	P	V	F	A	N	L	L	Y	S	Q	R	D	G	K	L
Secondary structure
SS confidence
Disorder																																																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	W	G	K	L	A	P	A	L	I	C	I	G	I	G	L	A	C	V	N	I	A	E	L	N	H	G	L	P	D	F	D	W	A	R	Y	T	S	G	I	V	L	A	L	V	S	V	V	C	W	A	W	Y	A	L	R	N	A	R	W
Secondary structure
SS confidence
Disorder																						?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	R	E	N	P	D	K	H	P	M	M	W	A	T	A	Q	A	L	V	T	L	P	V	S	L	I	G	Y	L	V	A	C	Y	W	L	N	T	Q	T	P	D	F	S	L	P	F	G	P	R	P	L	V	F	I	S	L	M	V	A	I
Secondary structure
SS confidence
Disorder			?					?		?																									?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		A	V	L	C	S	W	V	G	A	L	C	W	N	V	A	S	Q	L	L	P	T	V	I	L	G	P	L	I	V	F	E	T	L	A	G	L	L	Y	T	F	L	L	R	Q	Q	M	P	P	L	M	T	L	S	G	I	A	L	L	V	I
Secondary structure
SS confidence
Disorder																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.
Sequence		G	V	V	I	A	V	R	A	K	P	E	K	P	L	T	E	S	V	S	E	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 1s7b chain A Region: 240 - 314 Aligned: 75 Modelled: 75 Confidence: 97.8% Identity: 17% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 2i68 chain B Region: 244 - 307 Aligned: 58 Modelled: 64 Confidence: 87.1% Identity: 10% 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: 195 - 315 Aligned: 117 Modelled: 121 Confidence: 47.0% Identity: 9% 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 3aqp chain B Region: 238 - 320 Aligned: 83 Modelled: 83 Confidence: 46.7% 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 PDB 2knc chain A Region: 289 - 320 Aligned: 32 Modelled: 32 Confidence: 45.0% Identity: 34% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2b2h chain A Region: 2 - 206 Aligned: 194 Modelled: 194 Confidence: 44.2% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 2jp3 chain A Region: 292 - 321 Aligned: 30 Modelled: 30 Confidence: 22.9% Identity: 20% 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 1pw4 chain A Region: 1 - 320 Aligned: 304 Modelled: 304 Confidence: 19.5% Identity: 14% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1u7g chain A Region: 2 - 207 Aligned: 195 Modelled: 195 Confidence: 17.3% Identity: 12% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 1iwg chain A domain 7 Region: 237 - 320 Aligned: 84 Modelled: 84 Confidence: 7.4% 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 1iwg chain A domain 8 Region: 237 - 321 Aligned: 85 Modelled: 85 Confidence: 7.4% Identity: 16% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 2jwa chain A Region: 296 - 317 Aligned: 22 Modelled: 22 Confidence: 6.7% Identity: 23% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 2k1a chain A Region: 289 - 313 Aligned: 25 Modelled: 25 Confidence: 6.6% Identity: 36% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 2oar chain A domain 1 Region: 292 - 320 Aligned: 29 Modelled: 29 Confidence: 6.3% Identity: 10% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2jo1 chain A Region: 289 - 320 Aligned: 32 Modelled: 32 Confidence: 6.1% Identity: 9% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 3rko chain N Region: 28 - 312 Aligned: 269 Modelled: 269 Confidence: 5.8% Identity: 11% 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 3b9y chain A Region: 39 - 207 Aligned: 162 Modelled: 169 Confidence: 5.6% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 1 d1s7ba_ 2 c2i68B_ 3 c3rkoF_ 4 c3aqpB_ 5 c2kncA_ 6 c2b2hA_ 7 c2jp3A_ 8 d1pw4a_ 9 d1u7ga_ 10 d1iwga7 11 d1iwga8 12 c2jwaA_ 13 c2k1aA_ 14 d2oara1 15 c2jo1A_ 16 c3rkoN_ 17 c3b9yA_

Detailed template information

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

1 d1s7ba_ 97.8 17 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 c2i68B_ 87.1 10 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_ 47.0 9 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 c3aqpB_ 46.7 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 5 c2kncA_ 45.0 34 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 6 c2b2hA_ 44.2 11 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 7 c2jp3A_ 22.9 20 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 d1pw4a_ 19.5 14 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 9 d1u7ga_ 17.3 12 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 10 d1iwga7 7.4 13 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 11 d1iwga8 7.4 16 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 12 c2jwaA_ 6.7 23 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 13 c2k1aA_ 6.6 36 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 14 d2oara1 6.3 10 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 15 c2jo1A_ 6.1 9 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 16 c3rkoN_ 5.8 11 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 17 c3b9yA_ 5.6 12 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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