Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	F	T	F	S	P	S	R	H	D	G	P	G	T	E	V	Y	G	R	P	P	G	I	L	S	A	Q	L	S	Y	P	A	A	A	P	P	A	V	F	F	P	G	A	D	F	P	G	T	Y	S	F	R	S	Y	P	Q	N	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?	?	?	?		?	?	?	?											?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.
Sequence		W	I	T	V	A	P	L	L	R	E	K	A	L	L	T	A
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 1y0k chain A domain 1 Region: 27 - 72 Aligned: 46 Modelled: 46 Confidence: 28.9% Identity: 35% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: PA4535-like Phyre2 PDB 2dex chain X domain 1 Region: 42 - 53 Aligned: 12 Modelled: 12 Confidence: 14.9% Identity: 50% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Peptidylarginine deiminase Pad4, middle domain Family: Peptidylarginine deiminase Pad4, middle domain Phyre2 PDB 1nhp chain A domain 2 Region: 43 - 56 Aligned: 14 Modelled: 14 Confidence: 6.9% Identity: 36% Fold: FAD/NAD(P)-binding domain Superfamily: FAD/NAD(P)-binding domain Family: FAD/NAD-linked reductases, N-terminal and central domains Phyre2 PDB 3nez chain B Region: 22 - 54 Aligned: 30 Modelled: 33 Confidence: 5.8% Identity: 33% PDB header:fluorescent protein Chain: B: PDB Molecule:mrojoa; PDBTitle: mrojoa Phyre2 PDB 2icr chain D Region: 22 - 54 Aligned: 30 Modelled: 33 Confidence: 5.2% Identity: 33% PDB header:fluorescent protein Chain: D: PDB Molecule:red fluorescent protein zoanrfp; PDBTitle: red fluorescent protein zrfp574 from zoanthus sp. Phyre2 PDB 1wqs chain A Region: 1 - 40 Aligned: 40 Modelled: 40 Confidence: 5.0% Identity: 25% PDB header:hydrolase Chain: A: PDB Molecule:3c-like protease; PDBTitle: crystal structure of norovirus 3c-like protease Phyre2 PDB 2vov chain A Region: 4 - 35 Aligned: 32 Modelled: 32 Confidence: 5.0% Identity: 34% PDB header:metal-binding protein Chain: A: PDB Molecule:surface-associated protein; PDBTitle: an oxidized tryptophan facilitates copper-binding in2 methylococcus capsulatus secreted protein mope. the3 stucture of wild-type mope to 1.35aa Phyre2 1 d1y0ka1 2 d2dexx1 3 d1nhpa2 4 c3nezB_ 5 c2icrD_ 6 c1wqsA_ 7 c2vovA_

Detailed template information

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

1 d1y0ka1 28.9 35 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:PA4535-like 2 d2dexx1 14.9 50 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Peptidylarginine deiminase Pad4, middle domain Family:Peptidylarginine deiminase Pad4, middle domain 3 d1nhpa2 6.9 36 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains 4 c3nezB_ 5.8 33 PDB header:fluorescent protein Chain: B: PDB Molecule:mrojoa; PDBTitle: mrojoa 5 c2icrD_ 5.2 33 PDB header:fluorescent protein Chain: D: PDB Molecule:red fluorescent protein zoanrfp; PDBTitle: red fluorescent protein zrfp574 from zoanthus sp. 6 c1wqsA_ 5.0 25 PDB header:hydrolase Chain: A: PDB Molecule:3c-like protease; PDBTitle: crystal structure of norovirus 3c-like protease 7 c2vovA_ 5.0 34 PDB header:metal-binding protein Chain: A: PDB Molecule:surface-associated protein; PDBTitle: an oxidized tryptophan facilitates copper-binding in2 methylococcus capsulatus secreted protein mope. the3 stucture of wild-type mope to 1.35aa

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