Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	T	L	N	I	I	W	Q	Y	L	R	A	F	V	L	I	Y	A	C	L	Y	A	G	I	F	I	A	S	L	L	P	V	T	I	P	G	S	I	I	G	M	L	I	L	F	V	L	L	A	L	Q	I	L	P	A	K	W	V
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	P	G	C	Y	V	L	I	R	Y	M	A	L	L	F	V	P	I	G	V	G	V	M	Q	Y	F	D	L	L	R	A	Q	F	G	P	V	V	V	S	C	A	V	S	T	L	V	V	F	L	V	V	S	W	S	S	Q	L	V	H	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.
Sequence		E	R	K	V	V	G	Q	K	G	S	E	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 2knc chain A Region: 93 - 132 Aligned: 40 Modelled: 40 Confidence: 28.1% Identity: 15% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1fft chain B domain 2 Region: 90 - 132 Aligned: 43 Modelled: 43 Confidence: 15.0% Identity: 9% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1iwg chain A domain 8 Region: 71 - 125 Aligned: 55 Modelled: 55 Confidence: 12.3% 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 1vek chain A Region: 60 - 71 Aligned: 12 Modelled: 12 Confidence: 10.2% Identity: 25% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 2l2t chain A Region: 95 - 128 Aligned: 34 Modelled: 34 Confidence: 9.8% Identity: 9% 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 2oar chain A domain 1 Region: 101 - 132 Aligned: 32 Modelled: 32 Confidence: 7.3% Identity: 13% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2cpw chain A domain 1 Region: 60 - 70 Aligned: 11 Modelled: 11 Confidence: 6.1% Identity: 27% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 1 c2kncA_ 2 d1fftb2 3 d1iwga8 4 d1veka_ 5 c2l2tA_ 6 d2oara1 7 d2cpwa1

Detailed template information

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

1 c2kncA_ 28.1 15 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 d1fftb2 15.0 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 3 d1iwga8 12.3 13 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 4 d1veka_ 10.2 25 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 5 c2l2tA_ 9.8 9 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 d2oara1 7.3 13 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 7 d2cpwa1 6.1 27 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain

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