Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	V	L	G	N	I	L	W	W	A	F	V	G	F	M	A	Y	A	T	L	I	K	P	D	N	T	D	P	A	V	V	N	Y	E	E	P	L	P	M	E	L	A	N	Y	G	E	P	G	E	G	A	K	I	M	N	A	A	K	I
Secondary structure
SS confidence
Disorder		?	?																					?							?	?	?	?	?										?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	G	R	D	Y	A	W	K	H	V	K	E	D	R	L	P	C	L	F	A	A	G	V	V	A	D	N	I	L	V	K	Y	H	F	S	N	E	T	E	F	K	L	K	A	A	A	V	R	E	C	A	N	V	A	E	N	N	G	F	V
Secondary structure
SS confidence
Disorder										?														?	?														?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130
Sequence		L	V	G	R	V	F	E	K	R	N
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 2gqb chain A domain 1 Region: 24 - 72 Aligned: 49 Modelled: 49 Confidence: 11.2% Identity: 22% Fold: RPA2825-like Superfamily: RPA2825-like Family: RPA2825-like Phyre2 PDB 2v6z chain M Region: 95 - 111 Aligned: 17 Modelled: 17 Confidence: 7.8% Identity: 41% PDB header:transferase Chain: M: PDB Molecule:dna polymerase epsilon subunit 2; PDBTitle: solution structure of amino terminal domain of human dna2 polymerase epsilon subunit b Phyre2 PDB 3lyv chain F Region: 119 - 130 Aligned: 12 Modelled: 12 Confidence: 7.3% Identity: 17% PDB header:chaperone Chain: F: PDB Molecule:ribosome-associated factor y; PDBTitle: crystal structure of a domain of ribosome-associated factor y from2 streptococcus pyogenes serotype m6. northeast structural genomics3 consortium target id dr64a Phyre2 PDB 2h3o chain A Region: 9 - 28 Aligned: 20 Modelled: 19 Confidence: 7.1% Identity: 25% PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices Phyre2 PDB 3haz chain A Region: 46 - 106 Aligned: 59 Modelled: 61 Confidence: 6.5% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:proline dehydrogenase; PDBTitle: crystal structure of bifunctional proline utilization a2 (puta) protein Phyre2 PDB 3h3i chain A Region: 81 - 98 Aligned: 18 Modelled: 18 Confidence: 6.1% Identity: 28% PDB header:lipid binding protein Chain: A: PDB Molecule:putative lipid binding protein; PDBTitle: crystal structure of a putative lipid binding protein (bt_2261) from2 bacteroides thetaiotaomicron vpi-5482 at 2.20 a resolution Phyre2 PDB 1waz chain A Region: 9 - 23 Aligned: 15 Modelled: 15 Confidence: 5.8% Identity: 33% PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles Phyre2 1 d2gqba1 2 c2v6zM_ 3 c3lyvF_ 4 c2h3oA_ 5 c3hazA_ 6 c3h3iA_ 7 c1wazA_

Detailed template information

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

1 d2gqba1 11.2 22 Fold:RPA2825-like Superfamily:RPA2825-like Family:RPA2825-like 2 c2v6zM_ 7.8 41 PDB header:transferase Chain: M: PDB Molecule:dna polymerase epsilon subunit 2; PDBTitle: solution structure of amino terminal domain of human dna2 polymerase epsilon subunit b 3 c3lyvF_ 7.3 17 PDB header:chaperone Chain: F: PDB Molecule:ribosome-associated factor y; PDBTitle: crystal structure of a domain of ribosome-associated factor y from2 streptococcus pyogenes serotype m6. northeast structural genomics3 consortium target id dr64a 4 c2h3oA_ 7.1 25 PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices 5 c3hazA_ 6.5 15 PDB header:oxidoreductase Chain: A: PDB Molecule:proline dehydrogenase; PDBTitle: crystal structure of bifunctional proline utilization a2 (puta) protein 6 c3h3iA_ 6.1 28 PDB header:lipid binding protein Chain: A: PDB Molecule:putative lipid binding protein; PDBTitle: crystal structure of a putative lipid binding protein (bt_2261) from2 bacteroides thetaiotaomicron vpi-5482 at 2.20 a resolution 7 c1wazA_ 5.8 33 PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles

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