Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	T	Y	Y	Q	A	E	N	S	T	A	E	P	A	L	V	N	A	I	E	Q	G	L	R	A	Q	H	G	V	V	T	E	D	D	I	L	M	E	L	T	K	W	V	E	A	S	D	N	D	I	L	S	D	I	Y	Q	Q	T	I
Secondary structure
SS confidence
Disorder		?	?	?			?	?	?	?			?															?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.
Sequence		N	Y	V	V	S	G	Q	H	P	T	L
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 2oxl chain A Region: 12 - 64 Aligned: 53 Modelled: 53 Confidence: 72.0% Identity: 19% PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance Phyre2 PDB 2bid chain A Region: 36 - 63 Aligned: 28 Modelled: 28 Confidence: 31.9% Identity: 25% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1ddb chain A Region: 36 - 63 Aligned: 28 Modelled: 28 Confidence: 30.9% Identity: 29% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1r8j chain A domain 2 Region: 14 - 51 Aligned: 38 Modelled: 38 Confidence: 8.6% Identity: 13% Fold: Flavodoxin-like Superfamily: CheY-like Family: N-terminal domain of the circadian clock protein KaiA Phyre2 PDB 2uwj chain E Region: 1 - 26 Aligned: 26 Modelled: 26 Confidence: 8.5% Identity: 31% PDB header:chaperone Chain: E: PDB Molecule:type iii export protein psce; PDBTitle: structure of the heterotrimeric complex which regulates2 type iii secretion needle formation Phyre2 PDB 3bbz chain A Region: 10 - 60 Aligned: 36 Modelled: 39 Confidence: 7.8% Identity: 53% PDB header:viral protein, replication Chain: A: PDB Molecule:p protein; PDBTitle: structure of the nucleocapsid-binding domain from the mumps2 virus phosphoprotein Phyre2 PDB 3us8 chain A Region: 34 - 55 Aligned: 22 Modelled: 21 Confidence: 7.2% Identity: 50% PDB header:oxidoreductase Chain: A: PDB Molecule:isocitrate dehydrogenase [nadp]; PDBTitle: crystal structure of an isocitrate dehydrogenase from sinorhizobium2 meliloti 1021 Phyre2 PDB 2a40 chain C Region: 10 - 28 Aligned: 19 Modelled: 19 Confidence: 6.3% Identity: 37% PDB header:structural protein Chain: C: PDB Molecule:wiskott-aldrich syndrome protein family member 2; PDBTitle: ternary complex of the wh2 domain of wave with actin-dnase i Phyre2 PDB 2a40 chain F Region: 10 - 28 Aligned: 19 Modelled: 19 Confidence: 6.3% Identity: 37% PDB header:structural protein Chain: F: PDB Molecule:wiskott-aldrich syndrome protein family member 2; PDBTitle: ternary complex of the wh2 domain of wave with actin-dnase i Phyre2 1 c2oxlA_ 2 d2bida_ 3 d1ddba_ 4 d1r8ja2 5 c2uwjE_ 6 c3bbzA_ 7 c3us8A_ 8 c2a40C_ 9 c2a40F_

Detailed template information

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

1 c2oxlA_ 72.0 19 PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance 2 d2bida_ 31.9 25 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 3 d1ddba_ 30.9 29 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 4 d1r8ja2 8.6 13 Fold:Flavodoxin-like Superfamily:CheY-like Family:N-terminal domain of the circadian clock protein KaiA 5 c2uwjE_ 8.5 31 PDB header:chaperone Chain: E: PDB Molecule:type iii export protein psce; PDBTitle: structure of the heterotrimeric complex which regulates2 type iii secretion needle formation 6 c3bbzA_ 7.8 53 PDB header:viral protein, replication Chain: A: PDB Molecule:p protein; PDBTitle: structure of the nucleocapsid-binding domain from the mumps2 virus phosphoprotein 7 c3us8A_ 7.2 50 PDB header:oxidoreductase Chain: A: PDB Molecule:isocitrate dehydrogenase [nadp]; PDBTitle: crystal structure of an isocitrate dehydrogenase from sinorhizobium2 meliloti 1021 8 c2a40C_ 6.3 37 PDB header:structural protein Chain: C: PDB Molecule:wiskott-aldrich syndrome protein family member 2; PDBTitle: ternary complex of the wh2 domain of wave with actin-dnase i 9 c2a40F_ 6.3 37 PDB header:structural protein Chain: F: PDB Molecule:wiskott-aldrich syndrome protein family member 2; PDBTitle: ternary complex of the wh2 domain of wave with actin-dnase i

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