Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	D	T	H	H	A	Q	G	P	G	K	S	V	L	G	I	G	Q	R	I	V	S	I	M	V	E	M	V	E	T	R	L	R	L	A	V	V	E	L	E	E	E	K	A	N	L	F	Q	L	L	L	M	L	G	L	T	M	L	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	A	F	G	L	M	S	L	M	V	L	I	I	W	A	V	D	P	Q	Y	R	L	N	A	M	I	A	T	T	V	V	L	L	L	L	A	L	I	G	G	I	W	T	L	R	K	S	R	K	S	T	L	L	R	H	T	R	H	E	L
Secondary structure
SS confidence
Disorder																																																?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.
Sequence		A	N	D	R	Q	L	L	E	E	E	S	R	E	Q
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 2oar chain A Region: 85 - 130 Aligned: 46 Modelled: 46 Confidence: 28.8% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 2z9f chain C Region: 98 - 127 Aligned: 30 Modelled: 30 Confidence: 24.8% Identity: 10% PDB header:biosynthetic protein Chain: C: PDB Molecule:cellulose synthase operon protein d; PDBTitle: crystal structure of axcesd protein from acetobacter xylinum Phyre2 PDB 2knc chain A Region: 80 - 113 Aligned: 34 Modelled: 34 Confidence: 8.3% Identity: 15% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3pjz chain A Region: 51 - 115 Aligned: 65 Modelled: 65 Confidence: 7.2% Identity: 14% PDB header:transport protein Chain: A: PDB Molecule:potassium uptake protein trkh; PDBTitle: crystal structure of the potassium transporter trkh from vibrio2 parahaemolyticus Phyre2 PDB 2klu chain A Region: 50 - 71 Aligned: 22 Modelled: 22 Confidence: 6.9% Identity: 23% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 2jo1 chain A Region: 77 - 132 Aligned: 56 Modelled: 56 Confidence: 6.8% 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 2bbj chain B Region: 15 - 106 Aligned: 83 Modelled: 92 Confidence: 6.7% Identity: 7% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 1 c2oarA_ 2 c2z9fC_ 3 c2kncA_ 4 c3pjzA_ 5 c2kluA_ 6 c2jo1A_ 7 c2bbjB_

Detailed template information

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

1 c2oarA_ 28.8 13 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 2 c2z9fC_ 24.8 10 PDB header:biosynthetic protein Chain: C: PDB Molecule:cellulose synthase operon protein d; PDBTitle: crystal structure of axcesd protein from acetobacter xylinum 3 c2kncA_ 8.3 15 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 4 c3pjzA_ 7.2 14 PDB header:transport protein Chain: A: PDB Molecule:potassium uptake protein trkh; PDBTitle: crystal structure of the potassium transporter trkh from vibrio2 parahaemolyticus 5 c2kluA_ 6.9 23 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 6 c2jo1A_ 6.8 9 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 7 c2bbjB_ 6.7 7 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter

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