Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	V	F	K	T	K	L	I	R	L	Q	L	T	A	E	E	L	D	A	L	T	A	D	F	I	S	Y	K	R	D	G	V	L	P	D	I	F	G	R	D	A	L	Y	D	D	S	F	T	W	P	L	I	K	F	E	R	V	A	H
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?						?	?																														?								?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	H	L	A	N	E	N	N	P	F	P	P	Q	L	R	Q	F	S	R	T	N	D	E	A	H	L	V	Y	C	Q	G	A	F	D	E	Q	A	W	L	L	I	A	I	L	K	P	E	P	H	K	L	A	R	D	N	N	Q	M	H	K
Secondary structure
SS confidence
Disorder							?		?	?		?	?																																											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.
Sequence		I	G	K	M	A	E	A	F	R	M	R	F
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 2fd6 chain U domain 2 Region: 80 - 95 Aligned: 16 Modelled: 16 Confidence: 16.1% Identity: 25% Fold: Snake toxin-like Superfamily: Snake toxin-like Family: Extracellular domain of cell surface receptors Phyre2 PDB 1v0d chain A Region: 88 - 127 Aligned: 38 Modelled: 40 Confidence: 15.3% Identity: 24% Fold: His-Me finger endonucleases Superfamily: His-Me finger endonucleases Family: Caspase-activated DNase, CAD (DffB, DFF40) Phyre2 PDB 1v0d chain A Region: 88 - 127 Aligned: 38 Modelled: 40 Confidence: 15.3% Identity: 24% PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad) Phyre2 PDB 2vu9 chain A Region: 12 - 47 Aligned: 33 Modelled: 36 Confidence: 12.3% Identity: 27% PDB header:hydrolase Chain: A: PDB Molecule:botulinum neurotoxin a heavy chain; PDBTitle: crystal structure of botulinum neurotoxin serotype a2 binding domain in complex with gt1b Phyre2 PDB 3ts3 chain D Region: 77 - 95 Aligned: 19 Modelled: 19 Confidence: 11.9% Identity: 32% PDB header:viral protein Chain: D: PDB Molecule:capsid polyprotein; PDBTitle: crystal structure of the projection domain of the turkey astrovirus2 capsid protein at 1.5 angstrom resolution Phyre2 PDB 2lfc chain A Region: 9 - 47 Aligned: 38 Modelled: 39 Confidence: 11.3% Identity: 32% PDB header:oxidoreductase Chain: A: PDB Molecule:fumarate reductase, flavoprotein subunit; PDBTitle: solution nmr structure of fumarate reductase flavoprotein subunit from2 lactobacillus plantarum, northeast structural genomics consortium3 target lpr145j Phyre2 PDB 2w0c chain T Region: 19 - 32 Aligned: 14 Modelled: 14 Confidence: 11.0% Identity: 50% PDB header:virus Chain: T: PDB Molecule:protein p6; PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2 Phyre2 PDB 1p5d chain X domain 1 Region: 2 - 44 Aligned: 43 Modelled: 43 Confidence: 9.7% Identity: 28% Fold: Phosphoglucomutase, first 3 domains Superfamily: Phosphoglucomutase, first 3 domains Family: Phosphoglucomutase, first 3 domains Phyre2 PDB 1hci chain A domain 1 Region: 14 - 37 Aligned: 24 Modelled: 24 Confidence: 8.8% Identity: 25% Fold: Spectrin repeat-like Superfamily: Spectrin repeat Family: Spectrin repeat Phyre2 PDB 1g03 chain A Region: 58 - 79 Aligned: 22 Modelled: 22 Confidence: 8.3% Identity: 32% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 2i9b chain F Region: 80 - 109 Aligned: 30 Modelled: 30 Confidence: 8.0% Identity: 20% PDB header:hydrolase Chain: F: PDB Molecule:urokinase plasminogen activator surface receptor; PDBTitle: crystal structure of atf-urokinase receptor complex Phyre2 PDB 1zy3 chain A domain 1 Region: 12 - 29 Aligned: 18 Modelled: 18 Confidence: 7.2% Identity: 44% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1o0l chain A Region: 14 - 29 Aligned: 16 Modelled: 16 Confidence: 5.9% Identity: 50% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1pgl chain 2 domain 2 Region: 68 - 93 Aligned: 26 Modelled: 26 Confidence: 5.9% Identity: 31% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 1ny7 chain 2 domain 2 Region: 68 - 93 Aligned: 26 Modelled: 26 Confidence: 5.7% Identity: 31% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 1eij chain A Region: 103 - 128 Aligned: 26 Modelled: 26 Confidence: 5.7% Identity: 19% Fold: RuvA C-terminal domain-like Superfamily: Double-stranded DNA-binding domain Family: Double-stranded DNA-binding domain Phyre2 PDB 3jtp chain B Region: 93 - 122 Aligned: 30 Modelled: 30 Confidence: 5.4% Identity: 10% PDB header:protein binding Chain: B: PDB Molecule:adapter protein meca 1; PDBTitle: crystal structure of the c-terminal domain of meca Phyre2 PDB 2cru chain A domain 1 Region: 103 - 128 Aligned: 26 Modelled: 26 Confidence: 5.2% Identity: 12% Fold: RuvA C-terminal domain-like Superfamily: Double-stranded DNA-binding domain Family: Double-stranded DNA-binding domain Phyre2 1 d2fd6u2 2 d1v0da_ 3 c1v0dA_ 4 c2vu9A_ 5 c3ts3D_ 6 c2lfcA_ 7 c2w0cT_ 8 d1p5dx1 9 d1hcia1 10 d1g03a_ 11 c2i9bF_ 12 d1zy3a1 13 d1o0la_ 14 d1pgl22 15 d1ny722 16 d1eija_ 17 c3jtpB_ 18 d2crua1

Detailed template information

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

1 d2fd6u2 16.1 25 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors 2 d1v0da_ 15.3 24 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:Caspase-activated DNase, CAD (DffB, DFF40) 3 c1v0dA_ 15.3 24 PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad) 4 c2vu9A_ 12.3 27 PDB header:hydrolase Chain: A: PDB Molecule:botulinum neurotoxin a heavy chain; PDBTitle: crystal structure of botulinum neurotoxin serotype a2 binding domain in complex with gt1b 5 c3ts3D_ 11.9 32 PDB header:viral protein Chain: D: PDB Molecule:capsid polyprotein; PDBTitle: crystal structure of the projection domain of the turkey astrovirus2 capsid protein at 1.5 angstrom resolution 6 c2lfcA_ 11.3 32 PDB header:oxidoreductase Chain: A: PDB Molecule:fumarate reductase, flavoprotein subunit; PDBTitle: solution nmr structure of fumarate reductase flavoprotein subunit from2 lactobacillus plantarum, northeast structural genomics consortium3 target lpr145j 7 c2w0cT_ 11.0 50 PDB header:virus Chain: T: PDB Molecule:protein p6; PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2 8 d1p5dx1 9.7 28 Fold:Phosphoglucomutase, first 3 domains Superfamily:Phosphoglucomutase, first 3 domains Family:Phosphoglucomutase, first 3 domains 9 d1hcia1 8.8 25 Fold:Spectrin repeat-like Superfamily:Spectrin repeat Family:Spectrin repeat 10 d1g03a_ 8.3 32 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 11 c2i9bF_ 8.0 20 PDB header:hydrolase Chain: F: PDB Molecule:urokinase plasminogen activator surface receptor; PDBTitle: crystal structure of atf-urokinase receptor complex 12 d1zy3a1 7.2 44 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 13 d1o0la_ 5.9 50 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 14 d1pgl22 5.9 31 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 15 d1ny722 5.7 31 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 16 d1eija_ 5.7 19 Fold:RuvA C-terminal domain-like Superfamily:Double-stranded DNA-binding domain Family:Double-stranded DNA-binding domain 17 c3jtpB_ 5.4 10 PDB header:protein binding Chain: B: PDB Molecule:adapter protein meca 1; PDBTitle: crystal structure of the c-terminal domain of meca 18 d2crua1 5.2 12 Fold:RuvA C-terminal domain-like Superfamily:Double-stranded DNA-binding domain Family:Double-stranded DNA-binding 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