Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.
Sequence		M	V	Q	C	V	R	H	F	V	L	P	R	L	K	K	D	A	G	L	P	F	F	F	P	L	I	T	H	S	Q	P	L	N	R	G	A	F	F	C	P	G	V	R	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 2wx6 chain B Region: 8 - 43 Aligned: 29 Modelled: 36 Confidence: 40.1% Identity: 41% PDB header:oxidoreductase Chain: B: PDB Molecule:peroxidase ycdb; PDBTitle: x-ray crystallographic structure of e. coli apo-efeb Phyre2 PDB 2iiz chain A domain 1 Region: 25 - 43 Aligned: 19 Modelled: 17 Confidence: 18.3% Identity: 26% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: Dyp-type peroxidase-like Phyre2 PDB 1r2z chain A domain 3 Region: 33 - 40 Aligned: 8 Modelled: 8 Confidence: 9.2% Identity: 50% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins Phyre2 PDB 1k82 chain A domain 3 Region: 33 - 40 Aligned: 8 Modelled: 8 Confidence: 9.1% Identity: 38% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins Phyre2 PDB 1tdz chain A domain 3 Region: 33 - 41 Aligned: 9 Modelled: 9 Confidence: 8.7% Identity: 56% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins Phyre2 PDB 1k3x chain A domain 3 Region: 33 - 41 Aligned: 9 Modelled: 9 Confidence: 8.4% Identity: 44% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins Phyre2 PDB 1l1t chain A domain 3 Region: 33 - 40 Aligned: 8 Modelled: 8 Confidence: 8.3% Identity: 50% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins Phyre2 PDB 3qns chain A Region: 25 - 43 Aligned: 19 Modelled: 19 Confidence: 7.6% Identity: 21% PDB header:oxidoreductase Chain: A: PDB Molecule:dyp peroxidase; PDBTitle: dypb from rhodococcus jostii rha1, crystal form 2 Phyre2 PDB 1ee8 chain A domain 3 Region: 33 - 41 Aligned: 9 Modelled: 9 Confidence: 7.5% Identity: 56% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins Phyre2 1 c2wx6B_ 2 d2iiza1 3 d1r2za3 4 d1k82a3 5 d1tdza3 6 d1k3xa3 7 d1l1ta3 8 c3qnsA_ 9 d1ee8a3

Detailed template information

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

1 c2wx6B_ 40.1 41 PDB header:oxidoreductase Chain: B: PDB Molecule:peroxidase ycdb; PDBTitle: x-ray crystallographic structure of e. coli apo-efeb 2 d2iiza1 18.3 26 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Dyp-type peroxidase-like 3 d1r2za3 9.2 50 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 4 d1k82a3 9.1 38 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 5 d1tdza3 8.7 56 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 6 d1k3xa3 8.4 44 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 7 d1l1ta3 8.3 50 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 8 c3qnsA_ 7.6 21 PDB header:oxidoreductase Chain: A: PDB Molecule:dyp peroxidase; PDBTitle: dypb from rhodococcus jostii rha1, crystal form 2 9 d1ee8a3 7.5 56 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins

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