Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	A	I	S	S	N	L	S	K	M	I	I	F	I	F	A	I	I	I	I	V	V	L	C	V	I	T	Y	L	Y	L	Y	K	D	E	S	L	V	S	K	H	Y	I	N	Y	M	A	I	P	E	N	D	G	V	F	T	W	L	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.
Sequence		D	F	F	P	H	V	A	V	D	I	S	I	Y	T	N	V	E	D	D	Y	F	F	L	I	F	P
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 2pmf chain A Region: 50 - 60 Aligned: 11 Modelled: 11 Confidence: 15.2% Identity: 18% PDB header:ligase Chain: A: PDB Molecule:glycyl-trna synthetase; PDBTitle: the crystal structure of a human glycyl-trna synthetase mutant Phyre2 PDB 1qhd chain A domain 2 Region: 49 - 75 Aligned: 27 Modelled: 27 Confidence: 12.9% Identity: 33% Fold: Viral protein domain Superfamily: Viral protein domain Family: Top domain of virus capsid protein Phyre2 PDB 1m1c chain A Region: 59 - 73 Aligned: 15 Modelled: 15 Confidence: 11.0% Identity: 47% Fold: L-A virus major coat protein Superfamily: L-A virus major coat protein Family: L-A virus major coat protein Phyre2 PDB 1m1c chain B Region: 59 - 73 Aligned: 15 Modelled: 15 Confidence: 11.0% Identity: 47% PDB header:virus Chain: B: PDB Molecule:major coat protein; PDBTitle: structure of the l-a virus Phyre2 PDB 1z8y chain N Region: 21 - 27 Aligned: 7 Modelled: 7 Confidence: 9.7% Identity: 43% PDB header:virus Chain: N: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses Phyre2 PDB 1z8y chain L Region: 21 - 27 Aligned: 7 Modelled: 7 Confidence: 9.7% Identity: 43% PDB header:virus Chain: L: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses Phyre2 PDB 1z8y chain J Region: 21 - 27 Aligned: 7 Modelled: 7 Confidence: 9.7% Identity: 43% PDB header:virus Chain: J: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses Phyre2 PDB 1z8y chain P Region: 21 - 27 Aligned: 7 Modelled: 7 Confidence: 9.7% Identity: 43% PDB header:virus Chain: P: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses Phyre2 PDB 3u2s chain C Region: 35 - 58 Aligned: 24 Modelled: 24 Confidence: 9.4% Identity: 25% PDB header:immune system Chain: C: PDB Molecule:envelope glycoprotein gp120; PDBTitle: crystal structure of pg9 fab in complex with v1v2 region from hiv-12 strain zm109 Phyre2 PDB 2hv2 chain A domain 1 Region: 49 - 58 Aligned: 10 Modelled: 10 Confidence: 7.7% Identity: 40% Fold: SCP-like Superfamily: SCP-like Family: EF1021 C-terminal domain-like Phyre2 PDB 1u5t chain B Region: 53 - 65 Aligned: 13 Modelled: 13 Confidence: 7.2% Identity: 15% PDB header:transport protein Chain: B: PDB Molecule:defective in vacuolar protein sorting; vps36p; PDBTitle: structure of the escrt-ii endosomal trafficking complex Phyre2 PDB 3m1c chain A Region: 38 - 57 Aligned: 19 Modelled: 20 Confidence: 6.7% Identity: 26% PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein h; PDBTitle: crystal structure of the conserved herpesvirus fusion regulator2 complex gh-gl Phyre2 PDB 2jwu chain A Region: 35 - 58 Aligned: 24 Modelled: 24 Confidence: 6.6% Identity: 25% PDB header:de novo protein Chain: A: PDB Molecule:gb88; PDBTitle: solution nmr structures of two designed proteins with 88%2 sequence identity but different fold and function Phyre2 PDB 2j3m chain A Region: 53 - 60 Aligned: 8 Modelled: 8 Confidence: 6.0% Identity: 38% PDB header:ligase Chain: A: PDB Molecule:prolyl-trna synthetase; PDBTitle: prolyl-trna synthetase from enterococcus faecalis complexed2 with atp, manganese and prolinol Phyre2 PDB 1sqw chain A domain 1 Region: 49 - 56 Aligned: 8 Modelled: 8 Confidence: 5.9% Identity: 25% Fold: PUA domain-like Superfamily: PUA domain-like Family: PUA domain Phyre2 PDB 1zs4 chain A domain 1 Region: 35 - 64 Aligned: 14 Modelled: 14 Confidence: 5.8% Identity: 43% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Bacteriophage CII protein Phyre2 PDB 1s6c chain B Region: 54 - 60 Aligned: 7 Modelled: 7 Confidence: 5.7% Identity: 71% PDB header:transport protein Chain: B: PDB Molecule:potassium voltage-gated channel subfamily d member 2; PDBTitle: crystal structure of the complex between kchip1 and kv4.2 n1-30 Phyre2 PDB 1ijd chain A Region: 57 - 63 Aligned: 7 Modelled: 7 Confidence: 5.5% Identity: 43% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 2i00 chain A domain 1 Region: 49 - 57 Aligned: 9 Modelled: 9 Confidence: 5.5% Identity: 33% Fold: SCP-like Superfamily: SCP-like Family: EF1021 C-terminal domain-like Phyre2 PDB 3a0h chain Y Region: 1 - 18 Aligned: 18 Modelled: 18 Confidence: 5.2% Identity: 39% PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 1 c2pmfA_ 2 d1qhda2 3 d1m1ca_ 4 c1m1cB_ 5 c1z8yN_ 6 c1z8yL_ 7 c1z8yJ_ 8 c1z8yP_ 9 c3u2sC_ 10 d2hv2a1 11 c1u5tB_ 12 c3m1cA_ 13 c2jwuA_ 14 c2j3mA_ 15 d1sqwa1 16 d1zs4a1 17 c1s6cB_ 18 d1ijda_ 19 d2i00a1 20 c3a0hY_ 21 22

Detailed template information

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

1 c2pmfA_ 15.2 18 PDB header:ligase Chain: A: PDB Molecule:glycyl-trna synthetase; PDBTitle: the crystal structure of a human glycyl-trna synthetase mutant 2 d1qhda2 12.9 33 Fold:Viral protein domain Superfamily:Viral protein domain Family:Top domain of virus capsid protein 3 d1m1ca_ 11.0 47 Fold:L-A virus major coat protein Superfamily:L-A virus major coat protein Family:L-A virus major coat protein 4 c1m1cB_ 11.0 47 PDB header:virus Chain: B: PDB Molecule:major coat protein; PDBTitle: structure of the l-a virus 5 c1z8yN_ 9.7 43 PDB header:virus Chain: N: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses 6 c1z8yL_ 9.7 43 PDB header:virus Chain: L: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses 7 c1z8yJ_ 9.7 43 PDB header:virus Chain: J: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses 8 c1z8yP_ 9.7 43 PDB header:virus Chain: P: PDB Molecule:spike glycoprotein e2; PDBTitle: mapping the e2 glycoprotein of alphaviruses 9 c3u2sC_ 9.4 25 PDB header:immune system Chain: C: PDB Molecule:envelope glycoprotein gp120; PDBTitle: crystal structure of pg9 fab in complex with v1v2 region from hiv-12 strain zm109 10 d2hv2a1 7.7 40 Fold:SCP-like Superfamily:SCP-like Family:EF1021 C-terminal domain-like 11 c1u5tB_ 7.2 15 PDB header:transport protein Chain: B: PDB Molecule:defective in vacuolar protein sorting; vps36p; PDBTitle: structure of the escrt-ii endosomal trafficking complex 12 c3m1cA_ 6.7 26 PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein h; PDBTitle: crystal structure of the conserved herpesvirus fusion regulator2 complex gh-gl 13 c2jwuA_ 6.6 25 PDB header:de novo protein Chain: A: PDB Molecule:gb88; PDBTitle: solution nmr structures of two designed proteins with 88%2 sequence identity but different fold and function 14 c2j3mA_ 6.0 38 PDB header:ligase Chain: A: PDB Molecule:prolyl-trna synthetase; PDBTitle: prolyl-trna synthetase from enterococcus faecalis complexed2 with atp, manganese and prolinol 15 d1sqwa1 5.9 25 Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain 16 d1zs4a1 5.8 43 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Bacteriophage CII protein 17 c1s6cB_ 5.7 71 PDB header:transport protein Chain: B: PDB Molecule:potassium voltage-gated channel subfamily d member 2; PDBTitle: crystal structure of the complex between kchip1 and kv4.2 n1-30 18 d1ijda_ 5.5 43 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 19 d2i00a1 5.5 33 Fold:SCP-like Superfamily:SCP-like Family:EF1021 C-terminal domain-like 20 c3a0hY_ 5.2 39 PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of i-substituted photosystem ii complex 21 c3a0hy_ not modelled 5.2 39 PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of i-substituted photosystem ii complex 22 c3fldA_ not modelled 5.1 26 PDB header:hydrolase Chain: A: PDB Molecule:protein trai; PDBTitle: crystal structure of the trai c-terminal 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

---

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