Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	I	I	R	Y	L	V	R	E	T	L	K	S	Q	L	A	I	L	F	I	L	L	L	I	F	F	C	Q	K	L	V	R	I	L	G	A	A	V	D	G	D	I	P	A	N	L	V	L	S	L	L	G	L	G	V	P	E	M	A
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	L	I	L	P	L	S	L	F	L	G	L	L	M	T	L	G	K	L	Y	T	E	S	E	I	T	V	M	H	A	C	G	L	S	K	A	V	L	V	K	A	A	M	I	L	A	V	F	T	A	I	V	A	A	V	N	V	M	W	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	P	W	S	S	R	H	Q	D	E	V	L	A	E	A	K	A	N	P	G	M	A	A	L	A	Q	G	Q	F	Q	Q	A	T	N	G	S	S	V	L	F	I	E	S	V	D	G	S	D	F	K	D	V	F	L	A	Q	I	R	P	K
Secondary structure
SS confidence
Disorder																		?	?	?	?	?	?	?	?	?		?	?																			?												?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	N	A	R	P	S	V	V	V	A	D	S	G	H	L	T	Q	L	R	D	G	S	Q	V	V	T	L	N	Q	G	T	R	F	E	G	T	A	L	L	R	D	F	R	I	T	D	F	Q	D	Y	Q	A	I	I	G	H	Q	A	V	A
Secondary structure
SS confidence
Disorder																																					?	?	?	?	?	?									?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	D	P	N	D	T	D	Q	M	D	M	R	T	L	W	N	T	D	T	D	R	A	R	A	E	L	N	W	R	I	T	L	V	F	T	V	F	M	M	A	L	M	V	V	P	L	S	V	V	N	P	R	Q	G	R	V	L	S	M	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?										?	?	?	?	?																												?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		P	A	M	L	L	Y	L	L	F	F	L	I	Q	T	S	L	K	S	N	G	G	K	G	K	L	D	P	T	L	W	M	W	T	V	N	L	I	Y	L	A	L	A	I	V	L	N	L	W	D	T	V	P	V	R	R	L	R	A	S	F
Secondary structure
SS confidence
Disorder																																																			?	?	?	?	?						?
Disorder confidence
		.	.	.	.	.	.
Sequence		S	R	K	G	A	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 2knc chain A Region: 332 - 363 Aligned: 31 Modelled: 32 Confidence: 11.1% Identity: 13% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2rdc chain A Region: 2 - 11 Aligned: 10 Modelled: 10 Confidence: 9.1% Identity: 40% PDB header:lipid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution Phyre2 PDB 2l9u chain A Region: 335 - 354 Aligned: 20 Modelled: 20 Confidence: 7.8% Identity: 15% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain Phyre2 PDB 2voy chain H Region: 44 - 83 Aligned: 40 Modelled: 40 Confidence: 7.2% Identity: 10% PDB header:hydrolase Chain: H: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 1f5q chain B domain 1 Region: 2 - 31 Aligned: 30 Modelled: 30 Confidence: 7.0% Identity: 3% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 1mhs chain A Region: 7 - 83 Aligned: 69 Modelled: 77 Confidence: 7.0% Identity: 14% PDB header:membrane protein, proton transport Chain: A: PDB Molecule:plasma membrane atpase; PDBTitle: model of neurospora crassa proton atpase Phyre2 PDB 2bbj chain B Region: 281 - 350 Aligned: 68 Modelled: 70 Confidence: 6.7% Identity: 16% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 2zxe chain A Region: 8 - 83 Aligned: 68 Modelled: 76 Confidence: 5.8% Identity: 13% PDB header:hydrolase/transport protein Chain: A: PDB Molecule:na, k-atpase alpha subunit; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state Phyre2 PDB 1rut chain X domain 1 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 38% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 1oed chain A Region: 6 - 125 Aligned: 120 Modelled: 120 Confidence: 5.2% Identity: 8% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 2kr6 chain A Region: 307 - 357 Aligned: 51 Modelled: 51 Confidence: 5.2% Identity: 20% PDB header:hydrolase Chain: A: PDB Molecule:presenilin-1; PDBTitle: solution structure of presenilin-1 ctf subunit Phyre2 1 c2kncA_ 2 c2rdcA_ 3 c2l9uA_ 4 c2voyH_ 5 d1f5qb1 6 c1mhsA_ 7 c2bbjB_ 8 c2zxeA_ 9 d1rutx1 10 d1oeda_ 11 c2kr6A_

Detailed template information

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

1 c2kncA_ 11.1 13 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 c2rdcA_ 9.1 40 PDB header:lipid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution 3 c2l9uA_ 7.8 15 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain 4 c2voyH_ 7.2 10 PDB header:hydrolase Chain: H: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 5 d1f5qb1 7.0 3 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 6 c1mhsA_ 7.0 14 PDB header:membrane protein, proton transport Chain: A: PDB Molecule:plasma membrane atpase; PDBTitle: model of neurospora crassa proton atpase 7 c2bbjB_ 6.7 16 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 8 c2zxeA_ 5.8 13 PDB header:hydrolase/transport protein Chain: A: PDB Molecule:na, k-atpase alpha subunit; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state 9 d1rutx1 5.6 38 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 10 d1oeda_ 5.2 8 Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore 11 c2kr6A_ 5.2 20 PDB header:hydrolase Chain: A: PDB Molecule:presenilin-1; PDBTitle: solution structure of presenilin-1 ctf subunit

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