Secondary structure and disorder prediction

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10

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20

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30

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40

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50

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60

Sequence

M

R

K

L

K

M

M

L

C

V

M

M

L

P

L

V

V

V

G

C

T

S

K

Q

S

V

S

Q

C

V

K

P

P

R

P

P

A

W

I

M

Q

P

P

P

D

W

Q

T

P

L

N

G

I

I

S

P

S

E

R

G

Secondary structure

SS confidence

Disorder

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Disorder confidence

Sequence

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 2wb1 chain Q Region: 46 - 58 Aligned: 13 Modelled: 13 Confidence: 13.0% Identity: 54% PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 PDB 2wb1 chain J Region: 46 - 58 Aligned: 13 Modelled: 13 Confidence: 12.2% Identity: 54% PDB header:transcription Chain: J: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 PDB 2c2a chain A domain 1 Region: 45 - 58 Aligned: 14 Modelled: 14 Confidence: 10.5% Identity: 36% Fold: ROP-like Superfamily: Homodimeric domain of signal transducing histidine kinase Family: Homodimeric domain of signal transducing histidine kinase Phyre2 PDB 1i8l chain C Region: 39 - 58 Aligned: 20 Modelled: 20 Confidence: 8.5% Identity: 35% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1tlt chain A domain 2 Region: 40 - 52 Aligned: 13 Modelled: 13 Confidence: 7.7% Identity: 38% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Glucose 6-phosphate dehydrogenase-like Phyre2 1 c2wb1Q_ 2 c2wb1J_ 3 d2c2aa1 4 d1i8lc_ 5 d1tlta2

Detailed template information

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

1 c2wb1Q_ 13.0 54 PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 2 c2wb1J_ 12.2 54 PDB header:transcription Chain: J: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 3 d2c2aa1 10.5 36 Fold:ROP-like Superfamily:Homodimeric domain of signal transducing histidine kinase Family:Homodimeric domain of signal transducing histidine kinase 4 d1i8lc_ 8.5 35 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 5 d1tlta2 7.7 38 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Glucose 6-phosphate dehydrogenase-like

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