Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	L	Q	V	S	H	Y	N	M	L	R	A	S	H	E	G	S	Q	K	V	V	V	R	T	V	I	T	V	R	F	V	P	G	A	A	I	A	K	S	I	L	Y	C	A	G	Q	L	V	F	K	E	S	G	H	H	L	T	G	T
Secondary structure
SS confidence
Disorder		?	?	?		?	?	?						?																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.
Sequence		D	T	I	Y	F	V	T	V	R	L	H	M	H	N	S	T	Y	S	S	I	F	C	F	S	M	S	V	L	L	S	R	R	R	V	S	G	D	L	T	C	R
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 1y6k chain R domain 2 Region: 50 - 99 Aligned: 50 Modelled: 50 Confidence: 23.4% Identity: 24% Fold: Immunoglobulin-like beta-sandwich Superfamily: Fibronectin type III Family: Fibronectin type III Phyre2 PDB 3gqq chain D Region: 57 - 74 Aligned: 18 Modelled: 15 Confidence: 19.4% Identity: 50% PDB header:splicing Chain: D: PDB Molecule:protein unc-119 homolog a; PDBTitle: crystal structure of the human retinal protein 4 (unc-1192 homolog a). northeast structural genomics consortium3 target hr3066a Phyre2 PDB 1sdw chain A domain 2 Region: 45 - 73 Aligned: 29 Modelled: 29 Confidence: 18.3% Identity: 17% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: PHM/PNGase F Family: Peptidylglycine alpha-hydroxylating monooxygenase, PHM Phyre2 PDB 2k8j chain X Region: 30 - 38 Aligned: 9 Modelled: 9 Confidence: 13.7% Identity: 78% PDB header:viral protein Chain: X: PDB Molecule:p7tm2; PDBTitle: solution structure of hcv p7 tm2 Phyre2 PDB 2k2w chain A Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 12.4% Identity: 27% PDB header:cell cycle Chain: A: PDB Molecule:recombination and dna repair protein; PDBTitle: second brct domain of nbs1 Phyre2 PDB 1r4x chain A domain 1 Region: 35 - 75 Aligned: 41 Modelled: 41 Confidence: 9.3% Identity: 22% Fold: Immunoglobulin-like beta-sandwich Superfamily: Clathrin adaptor appendage domain Family: Coatomer appendage domain Phyre2 PDB 2lka chain A Region: 43 - 47 Aligned: 5 Modelled: 5 Confidence: 9.2% Identity: 100% PDB header:toxin Chain: A: PDB Molecule:toxin ts16; PDBTitle: new tricks of an old fold: structural versatility of scorpion toxins2 with common cysteine spacing Phyre2 PDB 2rnr chain B domain 1 Region: 2 - 27 Aligned: 26 Modelled: 26 Confidence: 9.1% Identity: 23% Fold: PH domain-like barrel Superfamily: PH domain-like Family: TFIIH domain Phyre2 PDB 2li3 chain A Region: 43 - 47 Aligned: 5 Modelled: 5 Confidence: 8.3% Identity: 100% PDB header:toxin Chain: A: PDB Molecule:potassium channel toxin kappa-ktx3.1; PDBTitle: structural and functional analysis of a novel potassium toxin2 argentinean scorpion tityus trivittatus reveals a new kappa sub-3 family Phyre2 PDB 1pzd chain A domain 1 Region: 35 - 75 Aligned: 41 Modelled: 41 Confidence: 7.6% Identity: 22% Fold: Immunoglobulin-like beta-sandwich Superfamily: Clathrin adaptor appendage domain Family: Coatomer appendage domain Phyre2 PDB 1umg chain A Region: 31 - 53 Aligned: 23 Modelled: 23 Confidence: 6.3% Identity: 43% Fold: Sulfolobus fructose-1,6-bisphosphatase-like Superfamily: Sulfolobus fructose-1,6-bisphosphatase-like Family: Sulfolobus fructose-1,6-bisphosphatase-like Phyre2 PDB 1opm chain A Region: 45 - 73 Aligned: 29 Modelled: 29 Confidence: 6.2% Identity: 17% PDB header:oxidoreductase Chain: A: PDB Molecule:protein (peptidylglycine alpha-hydroxylating PDBTitle: oxidized (cu2+) peptidylglycine alpha-hydroxylating monooxygenase2 (phm) with bound substrate Phyre2 PDB 2dvk chain A Region: 38 - 69 Aligned: 32 Modelled: 32 Confidence: 5.7% Identity: 31% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0130 protein ape0816; PDBTitle: crystal structure of hypothetical protein from aeropyrum pernix Phyre2 PDB 1pzd chain A Region: 49 - 75 Aligned: 27 Modelled: 27 Confidence: 5.7% Identity: 30% PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:coatomer gamma subunit; PDBTitle: structural identification of a conserved appendage domain2 in the carboxyl-terminus of the copi gamma-subunit. Phyre2 1 d1y6kr2 2 c3gqqD_ 3 d1sdwa2 4 c2k8jX_ 5 c2k2wA_ 6 d1r4xa1 7 c2lkaA_ 8 d2rnrb1 9 c2li3A_ 10 d1pzda1 11 d1umga_ 12 c1opmA_ 13 c2dvkA_ 14 c1pzdA_

Detailed template information

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

1 d1y6kr2 23.4 24 Fold:Immunoglobulin-like beta-sandwich Superfamily:Fibronectin type III Family:Fibronectin type III 2 c3gqqD_ 19.4 50 PDB header:splicing Chain: D: PDB Molecule:protein unc-119 homolog a; PDBTitle: crystal structure of the human retinal protein 4 (unc-1192 homolog a). northeast structural genomics consortium3 target hr3066a 3 d1sdwa2 18.3 17 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:PHM/PNGase F Family:Peptidylglycine alpha-hydroxylating monooxygenase, PHM 4 c2k8jX_ 13.7 78 PDB header:viral protein Chain: X: PDB Molecule:p7tm2; PDBTitle: solution structure of hcv p7 tm2 5 c2k2wA_ 12.4 27 PDB header:cell cycle Chain: A: PDB Molecule:recombination and dna repair protein; PDBTitle: second brct domain of nbs1 6 d1r4xa1 9.3 22 Fold:Immunoglobulin-like beta-sandwich Superfamily:Clathrin adaptor appendage domain Family:Coatomer appendage domain 7 c2lkaA_ 9.2 100 PDB header:toxin Chain: A: PDB Molecule:toxin ts16; PDBTitle: new tricks of an old fold: structural versatility of scorpion toxins2 with common cysteine spacing 8 d2rnrb1 9.1 23 Fold:PH domain-like barrel Superfamily:PH domain-like Family:TFIIH domain 9 c2li3A_ 8.3 100 PDB header:toxin Chain: A: PDB Molecule:potassium channel toxin kappa-ktx3.1; PDBTitle: structural and functional analysis of a novel potassium toxin2 argentinean scorpion tityus trivittatus reveals a new kappa sub-3 family 10 d1pzda1 7.6 22 Fold:Immunoglobulin-like beta-sandwich Superfamily:Clathrin adaptor appendage domain Family:Coatomer appendage domain 11 d1umga_ 6.3 43 Fold:Sulfolobus fructose-1,6-bisphosphatase-like Superfamily:Sulfolobus fructose-1,6-bisphosphatase-like Family:Sulfolobus fructose-1,6-bisphosphatase-like 12 c1opmA_ 6.2 17 PDB header:oxidoreductase Chain: A: PDB Molecule:protein (peptidylglycine alpha-hydroxylating PDBTitle: oxidized (cu2+) peptidylglycine alpha-hydroxylating monooxygenase2 (phm) with bound substrate 13 c2dvkA_ 5.7 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0130 protein ape0816; PDBTitle: crystal structure of hypothetical protein from aeropyrum pernix 14 c1pzdA_ 5.7 30 PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:coatomer gamma subunit; PDBTitle: structural identification of a conserved appendage domain2 in the carboxyl-terminus of the copi gamma-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