Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	A	V	L	S	V	Q	G	A	S	A	P	V	K	K	K	S	F	F	S	K	F	T	R	L	N	M	L	R	L	A	R	A	V	I	P	A	A	V	L	M	M	F	F	P	Q	L	A	M	A	A	G	S	S	G	Q	D	L	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?										?					?	?																		?	?			?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	S	G	N	T	T	V	K	A	T	F	G	K	D	S	S	V	V	K	W	V	V	L	A	E	V	L	V	G	A	V	M	Y	M	M	T	K	N	V	K	F	L	A	G	F	A	I	I	S	V	F	I	A	V	G	M	A	V	V	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?					?																																																	?	?
Disorder confidence
		.
Sequence		L
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: 69 - 92 Aligned: 24 Modelled: 24 Confidence: 35.6% Identity: 29% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2k1a chain A Region: 73 - 92 Aligned: 20 Modelled: 20 Confidence: 23.4% Identity: 30% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 2voy chain B Region: 12 - 45 Aligned: 34 Modelled: 34 Confidence: 22.0% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 2jtw chain A Region: 16 - 36 Aligned: 21 Modelled: 21 Confidence: 7.3% Identity: 43% PDB header:membrane protein Chain: A: PDB Molecule:transmembrane helix 7 of yeast vatpase; PDBTitle: solution structure of tm7 bound to dpc micelles Phyre2 PDB 2yt9 chain A domain 2 Region: 20 - 32 Aligned: 13 Modelled: 13 Confidence: 6.1% Identity: 31% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 3dl8 chain F Region: 59 - 76 Aligned: 18 Modelled: 18 Confidence: 6.1% Identity: 33% PDB header:protein transport Chain: F: PDB Molecule:protein-export membrane protein secg; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 3da5 chain A Region: 12 - 23 Aligned: 12 Modelled: 12 Confidence: 6.1% Identity: 50% PDB header:rna binding protein Chain: A: PDB Molecule:argonaute; PDBTitle: crystal structure of piwi/argonaute/zwille(paz) domain from2 thermococcus thioreducens Phyre2 1 c2kncA_ 2 c2k1aA_ 3 c2voyB_ 4 c2jtwA_ 5 d2yt9a2 6 c3dl8F_ 7 c3da5A_

Detailed template information

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

1 c2kncA_ 35.6 29 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 c2k1aA_ 23.4 30 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 3 c2voyB_ 22.0 18 PDB header:hydrolase Chain: B: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 4 c2jtwA_ 7.3 43 PDB header:membrane protein Chain: A: PDB Molecule:transmembrane helix 7 of yeast vatpase; PDBTitle: solution structure of tm7 bound to dpc micelles 5 d2yt9a2 6.1 31 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 6 c3dl8F_ 6.1 33 PDB header:protein transport Chain: F: PDB Molecule:protein-export membrane protein secg; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 7 c3da5A_ 6.1 50 PDB header:rna binding protein Chain: A: PDB Molecule:argonaute; PDBTitle: crystal structure of piwi/argonaute/zwille(paz) domain from2 thermococcus thioreducens

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