Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	I	Q	G	I	E	G	V	I	S	Q	L	Q	A	T	A	M	S	A	R	A	Q	E	S	L	P	Q	P	T	I	S	F	A	G	Q	L	H	A	A	L	D	R	I	S	D	T	Q	T	A	A	R	T	Q	A	E	K	F	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.
Sequence		L	G	E	P	G	V	A	L	N	D	V	M	T	D	M	Q	K	A	S	V	S	M	Q	M	G	I	Q	V	R	N	K	L	V	A	A	Y	Q	E	V	M	S	M	Q	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 2cly chain A Region: 32 - 101 Aligned: 70 Modelled: 70 Confidence: 21.1% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:atp synthase b chain, mitochondrial; PDBTitle: subcomplex of the stator of bovine mitochondrial atp2 synthase Phyre2 PDB 2cly chain A domain 1 Region: 32 - 101 Aligned: 70 Modelled: 70 Confidence: 21.1% Identity: 17% Fold: ATP synthase B chain-like Superfamily: ATP synthase B chain-like Family: ATP synthase B chain-like Phyre2 PDB 2ido chain B domain 1 Region: 95 - 104 Aligned: 10 Modelled: 10 Confidence: 15.7% Identity: 40% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2ia9 chain A domain 1 Region: 83 - 100 Aligned: 18 Modelled: 18 Confidence: 13.5% Identity: 6% Fold: SpoVG-like Superfamily: SpoVG-like Family: SpoVG-like Phyre2 PDB 1se7 chain A Region: 95 - 104 Aligned: 10 Modelled: 10 Confidence: 13.3% Identity: 40% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2ae9 chain A domain 1 Region: 95 - 104 Aligned: 10 Modelled: 10 Confidence: 12.5% Identity: 40% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2wss chain T Region: 77 - 101 Aligned: 25 Modelled: 25 Confidence: 8.2% Identity: 20% PDB header:hydrolase Chain: T: PDB Molecule:atp synthase subunit b, mitochondrial; PDBTitle: the structure of the membrane extrinsic region of bovine2 atp synthase Phyre2 PDB 1kmi chain Z Region: 33 - 67 Aligned: 35 Modelled: 35 Confidence: 6.3% Identity: 17% PDB header:signaling protein Chain: Z: PDB Molecule:chemotaxis protein chez; PDBTitle: crystal structure of an e.coli chemotaxis protein, chez Phyre2 PDB 6pax chain A domain 1 Region: 86 - 98 Aligned: 13 Modelled: 13 Confidence: 6.1% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1rj9 chain B domain 1 Region: 68 - 92 Aligned: 25 Modelled: 25 Confidence: 5.5% Identity: 12% Fold: Four-helical up-and-down bundle Superfamily: Domain of the SRP/SRP receptor G-proteins Family: Domain of the SRP/SRP receptor G-proteins Phyre2 PDB 1k78 chain A domain 1 Region: 86 - 98 Aligned: 13 Modelled: 13 Confidence: 5.4% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 1 c2clyA_ 2 d2clya1 3 d2idob1 4 d2ia9a1 5 d1se7a_ 6 d2ae9a1 7 c2wssT_ 8 c1kmiZ_ 9 d6paxa1 10 d1rj9b1 11 d1k78a1

Detailed template information

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

1 c2clyA_ 21.1 17 PDB header:hydrolase Chain: A: PDB Molecule:atp synthase b chain, mitochondrial; PDBTitle: subcomplex of the stator of bovine mitochondrial atp2 synthase 2 d2clya1 21.1 17 Fold:ATP synthase B chain-like Superfamily:ATP synthase B chain-like Family:ATP synthase B chain-like 3 d2idob1 15.7 40 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 4 d2ia9a1 13.5 6 Fold:SpoVG-like Superfamily:SpoVG-like Family:SpoVG-like 5 d1se7a_ 13.3 40 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 6 d2ae9a1 12.5 40 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 7 c2wssT_ 8.2 20 PDB header:hydrolase Chain: T: PDB Molecule:atp synthase subunit b, mitochondrial; PDBTitle: the structure of the membrane extrinsic region of bovine2 atp synthase 8 c1kmiZ_ 6.3 17 PDB header:signaling protein Chain: Z: PDB Molecule:chemotaxis protein chez; PDBTitle: crystal structure of an e.coli chemotaxis protein, chez 9 d6paxa1 6.1 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 10 d1rj9b1 5.5 12 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 11 d1k78a1 5.4 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired 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