Secondary structure and disorder prediction

1

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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

F

E

F

Y

I

A

A

R

E

Q

K

E

T

G

H

P

G

I

F

S

R

Q

K

H

S

T

I

I

Y

V

I

C

L

L

L

I

C

L

W

F

A

G

M

V

L

V

G

G

Y

A

R

Q

L

W

V

L

W

I

V

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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80

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90

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100

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110

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120

Sequence

K

A

E

V

T

V

E

A

E

T

P

A

F

K

Q

S

T

Q

H

Y

F

F

K

K

Q

P

L

P

V

V

E

S

V

E

E

E

D

D

P

G

V

A

V

E

N

A

P

S

S

S

E

D

E

E

N

T

V

E

E

S

Secondary structure

SS confidence

Disorder

?

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?

?

?

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?

?

Disorder confidence

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130

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Sequence

E

E

K

A

G

L

R

E

R

V

K

N

A

L

N

E

L

E

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 2d46 chain A Region: 97 - 139 Aligned: 43 Modelled: 43 Confidence: 17.5% Identity: 23% PDB header:metal transport Chain: A: PDB Molecule:calcium channel, voltage-dependent, beta 4 PDBTitle: solution structure of the human beta4a-a domain Phyre2 PDB 3i31 chain A Region: 7 - 40 Aligned: 34 Modelled: 34 Confidence: 16.4% Identity: 18% PDB header:rna binding protein,hydrolase Chain: A: PDB Molecule:heat resistant rna dependent atpase; PDBTitle: hera helicase rna binding domain is an rrm fold Phyre2 PDB 1x9b chain A Region: 123 - 139 Aligned: 17 Modelled: 17 Confidence: 11.9% Identity: 29% Fold: Protozoan pheromone-like Superfamily: Hypothetical membrane protein Ta0354, soluble domain Family: Hypothetical membrane protein Ta0354, soluble domain Phyre2 PDB 1ft8 chain E Region: 72 - 83 Aligned: 12 Modelled: 12 Confidence: 10.5% Identity: 33% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Non-canonical RBD domain Phyre2 PDB 1zps chain A domain 1 Region: 7 - 22 Aligned: 16 Modelled: 16 Confidence: 8.6% Identity: 38% Fold: HisI-like Superfamily: HisI-like Family: HisI-like Phyre2 PDB 2fef chain A domain 2 Region: 33 - 45 Aligned: 13 Modelled: 12 Confidence: 8.5% Identity: 15% Fold: PA2201 C-terminal domain-like Superfamily: PA2201 C-terminal domain-like Family: PA2201 C-terminal domain-like Phyre2 PDB 1iml chain A domain 1 Region: 15 - 27 Aligned: 13 Modelled: 13 Confidence: 7.8% Identity: 15% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 2cu8 chain A domain 1 Region: 15 - 27 Aligned: 13 Modelled: 13 Confidence: 7.3% Identity: 15% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 2zjs chain E Region: 28 - 57 Aligned: 30 Modelled: 30 Confidence: 7.1% Identity: 20% PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment Phyre2 PDB 2cql chain A domain 1 Region: 78 - 98 Aligned: 21 Modelled: 21 Confidence: 6.9% Identity: 14% Fold: Ribosomal protein L6 Superfamily: Ribosomal protein L6 Family: Ribosomal protein L6 Phyre2 PDB 3bm3 chain A Region: 123 - 139 Aligned: 17 Modelled: 17 Confidence: 6.8% Identity: 35% PDB header:hydrolase/dna Chain: A: PDB Molecule:pspgi restriction endonuclease; PDBTitle: restriction endonuclease pspgi-substrate dna complex Phyre2 1 c2d46A_ 2 c3i31A_ 3 d1x9ba_ 4 d1ft8e_ 5 d1zpsa1 6 d2fefa2 7 d1imla1 8 d2cu8a1 9 c2zjsE_ 10 d2cqla1 11 c3bm3A_

Detailed template information

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

1 c2d46A_ 17.5 23 PDB header:metal transport Chain: A: PDB Molecule:calcium channel, voltage-dependent, beta 4 PDBTitle: solution structure of the human beta4a-a domain 2 c3i31A_ 16.4 18 PDB header:rna binding protein,hydrolase Chain: A: PDB Molecule:heat resistant rna dependent atpase; PDBTitle: hera helicase rna binding domain is an rrm fold 3 d1x9ba_ 11.9 29 Fold:Protozoan pheromone-like Superfamily:Hypothetical membrane protein Ta0354, soluble domain Family:Hypothetical membrane protein Ta0354, soluble domain 4 d1ft8e_ 10.5 33 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Non-canonical RBD domain 5 d1zpsa1 8.6 38 Fold:HisI-like Superfamily:HisI-like Family:HisI-like 6 d2fefa2 8.5 15 Fold:PA2201 C-terminal domain-like Superfamily:PA2201 C-terminal domain-like Family:PA2201 C-terminal domain-like 7 d1imla1 7.8 15 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 8 d2cu8a1 7.3 15 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 9 c2zjsE_ 7.1 20 PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment 10 d2cqla1 6.9 14 Fold:Ribosomal protein L6 Superfamily:Ribosomal protein L6 Family:Ribosomal protein L6 11 c3bm3A_ 6.8 35 PDB header:hydrolase/dna Chain: A: PDB Molecule:pspgi restriction endonuclease; PDBTitle: restriction endonuclease pspgi-substrate dna complex

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