Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	P	L	R	Q	Q	N	R	Q	I	I	S	Y	V	P	R	T	E	P	A	P	P	E	H	A	I	K	M	D	S	F	R	D	V	W	M	L	R	G	K	Y	V	A	F	V	L	M	G	E	S	F	L	R	S	P	A	F	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?			?	?															?	?																																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80
Sequence		V	P	E	S	A	Q	R	W	A	N	Q	I	R	Q	E	G	E	V	T	E
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 2bn8 chain A Region: 14 - 80 Aligned: 67 Modelled: 67 Confidence: 100.0% Identity: 100% PDB header:cell cycle protein Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure and interactions of the e.coli cell2 division activator protein ceda Phyre2 PDB 2d35 chain A Region: 19 - 80 Aligned: 62 Modelled: 62 Confidence: 100.0% Identity: 100% PDB header:cell cycle Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure of cell division reactivation factor,2 ceda Phyre2 PDB 1udx chain A domain 3 Region: 36 - 76 Aligned: 35 Modelled: 41 Confidence: 27.3% Identity: 29% Fold: Obg GTP-binding protein C-terminal domain Superfamily: Obg GTP-binding protein C-terminal domain Family: Obg GTP-binding protein C-terminal domain Phyre2 PDB 1pii chain A Region: 7 - 57 Aligned: 48 Modelled: 51 Confidence: 22.4% Identity: 15% PDB header:bifunctional(isomerase and synthase) Chain: A: PDB Molecule:n-(5'phosphoribosyl)anthranilate isomerase; PDBTitle: three-dimensional structure of the bifunctional enzyme2 phosphoribosylanthranilate isomerase:3 indoleglycerolphosphate synthase from escherichia coli4 refined at 2.0 angstroms resolution Phyre2 PDB 1hh4 chain E Region: 14 - 45 Aligned: 26 Modelled: 32 Confidence: 11.6% Identity: 46% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: RhoGDI-like Phyre2 PDB 1ds6 chain B Region: 14 - 45 Aligned: 26 Modelled: 32 Confidence: 8.9% Identity: 46% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: RhoGDI-like Phyre2 PDB 1ajw chain A Region: 14 - 45 Aligned: 30 Modelled: 32 Confidence: 8.1% Identity: 33% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: RhoGDI-like Phyre2 PDB 1rho chain A Region: 14 - 45 Aligned: 30 Modelled: 32 Confidence: 7.5% Identity: 30% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: RhoGDI-like Phyre2 PDB 2o2k chain A Region: 28 - 79 Aligned: 52 Modelled: 52 Confidence: 6.9% Identity: 27% PDB header:transferase Chain: A: PDB Molecule:methionine synthase; PDBTitle: crystal structure of the activation domain of human2 methionine synthase isoform/mutant d963e/k1071n Phyre2 PDB 1bds chain A Region: 35 - 41 Aligned: 7 Modelled: 7 Confidence: 6.5% Identity: 71% Fold: Defensin-like Superfamily: Defensin-like Family: Defensin Phyre2 PDB 1fso chain A Region: 14 - 45 Aligned: 30 Modelled: 32 Confidence: 5.7% Identity: 30% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: RhoGDI-like Phyre2 PDB 1x60 chain A Region: 58 - 76 Aligned: 19 Modelled: 19 Confidence: 5.5% Identity: 32% PDB header:hydrolase Chain: A: PDB Molecule:sporulation-specific n-acetylmuramoyl-l-alanine PDBTitle: solution structure of the peptidoglycan binding domain of2 b. subtilis cell wall lytic enzyme cwlc Phyre2 PDB 1q45 chain A Region: 29 - 80 Aligned: 43 Modelled: 52 Confidence: 5.3% Identity: 16% Fold: TIM beta/alpha-barrel Superfamily: FMN-linked oxidoreductases Family: FMN-linked oxidoreductases Phyre2 1 c2bn8A_ 2 c2d35A_ 3 d1udxa3 4 c1piiA_ 5 d1hh4e_ 6 d1ds6b_ 7 d1ajwa_ 8 d1rhoa_ 9 c2o2kA_ 10 d1bdsa_ 11 d1fsoa_ 12 c1x60A_ 13 d1q45a_

Detailed template information

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

1 c2bn8A_ 100.0 100 PDB header:cell cycle protein Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure and interactions of the e.coli cell2 division activator protein ceda 2 c2d35A_ 100.0 100 PDB header:cell cycle Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure of cell division reactivation factor,2 ceda 3 d1udxa3 27.3 29 Fold:Obg GTP-binding protein C-terminal domain Superfamily:Obg GTP-binding protein C-terminal domain Family:Obg GTP-binding protein C-terminal domain 4 c1piiA_ 22.4 15 PDB header:bifunctional(isomerase and synthase) Chain: A: PDB Molecule:n-(5'phosphoribosyl)anthranilate isomerase; PDBTitle: three-dimensional structure of the bifunctional enzyme2 phosphoribosylanthranilate isomerase:3 indoleglycerolphosphate synthase from escherichia coli4 refined at 2.0 angstroms resolution 5 d1hh4e_ 11.6 46 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 6 d1ds6b_ 8.9 46 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 7 d1ajwa_ 8.1 33 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 8 d1rhoa_ 7.5 30 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 9 c2o2kA_ 6.9 27 PDB header:transferase Chain: A: PDB Molecule:methionine synthase; PDBTitle: crystal structure of the activation domain of human2 methionine synthase isoform/mutant d963e/k1071n 10 d1bdsa_ 6.5 71 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 11 d1fsoa_ 5.7 30 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 12 c1x60A_ 5.5 32 PDB header:hydrolase Chain: A: PDB Molecule:sporulation-specific n-acetylmuramoyl-l-alanine PDBTitle: solution structure of the peptidoglycan binding domain of2 b. subtilis cell wall lytic enzyme cwlc 13 d1q45a_ 5.3 16 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases

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