Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Y	I	Y	W	I	L	L	G	L	A	I	A	T	E	I	T	G	T	L	S	M	K	W	A	S	V	S	E	G	N	G	G	F	I	L	M	L	V	M	I	S	L	S	Y	I	F	L	S	F	A	V	K	K	I	A	L	G	V	A
Secondary structure
SS confidence
Disorder		?	?																								?	?																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	A	L	W	E	G	I	G	I	L	F	I	T	L	F	S	V	L	L	F	D	E	S	L	S	L	M	K	I	A	G	L	T	T	L	V	A	G	I	V	L	I	K	S	G	T	R	K	A	R	K	P	E	L	E	V	N	H	G	A
Secondary structure
SS confidence
Disorder																																													?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.
Sequence		V
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: 6 - 110 Aligned: 105 Modelled: 105 Confidence: 100.0% Identity: 31% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 2i68 chain B Region: 5 - 105 Aligned: 78 Modelled: 101 Confidence: 99.8% Identity: 36% 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 3mp7 chain B Region: 80 - 102 Aligned: 23 Modelled: 23 Confidence: 23.9% Identity: 22% PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes Phyre2 PDB 2nr1 chain A Region: 1 - 15 Aligned: 15 Modelled: 15 Confidence: 5.3% Identity: 27% PDB header:receptor Chain: A: PDB Molecule:nr1 m2; PDBTitle: transmembrane segment 2 of nmda receptor nr1, nmr, 102 structures Phyre2 PDB 2axt chain J domain 1 Region: 68 - 81 Aligned: 14 Modelled: 14 Confidence: 5.1% Identity: 14% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein J, PsbJ Family: PsbJ-like Phyre2 1 d1s7ba_ 2 c2i68B_ 3 c3mp7B_ 4 c2nr1A_ 5 d2axtj1

Detailed template information

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

1 d1s7ba_ 100.0 31 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 c2i68B_ 99.8 36 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 c3mp7B_ 23.9 22 PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes 4 c2nr1A_ 5.3 27 PDB header:receptor Chain: A: PDB Molecule:nr1 m2; PDBTitle: transmembrane segment 2 of nmda receptor nr1, nmr, 102 structures 5 d2axtj1 5.1 14 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like

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