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

G

R

I

A

Y

K

S

V

I

M

L

S

L

Q

P

S

C

V

K

S

N

C

Q

G

D

G

D

V

P

G

Q

N

T

R

G

A

P

S

P

F

L

F

P

F

S

V

F

S

D

P

I

H

P

G

I

T

P

I

L

Secondary structure

SS confidence

Disorder

?

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?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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80

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90

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Sequence

P

K

T

A

N

Q

P

S

A

R

A

T

T

G

L

I

R

D

P

C

C

K

T

Y

L

Y

V

F

G

F

T

R

N

N

A

Secondary structure

SS confidence

Disorder

?

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?

?

?

?

?

?

?

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?

?

?

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 1sdd chain B domain 1 Region: 50 - 86 Aligned: 33 Modelled: 33 Confidence: 28.4% Identity: 21% Fold: Cupredoxin-like Superfamily: Cupredoxins Family: Multidomain cupredoxins Phyre2 PDB 1tvt chain A Region: 27 - 36 Aligned: 10 Modelled: 10 Confidence: 17.7% Identity: 80% PDB header:transcription regulation Chain: A: PDB Molecule:transactivator protein; PDBTitle: structure of the equine infectious anemia virus tat protein Phyre2 PDB 1mkf chain A Region: 46 - 95 Aligned: 50 Modelled: 50 Confidence: 17.1% Identity: 22% Fold: Viral chemokine binding protein m3 Superfamily: Viral chemokine binding protein m3 Family: Viral chemokine binding protein m3 Phyre2 PDB 1kqh chain A Region: 78 - 85 Aligned: 8 Modelled: 8 Confidence: 16.5% Identity: 75% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Spider toxins Phyre2 PDB 3nsw chain A Region: 60 - 94 Aligned: 33 Modelled: 35 Confidence: 9.0% Identity: 45% PDB header:immune system Chain: A: PDB Molecule:excretory-secretory protein 2; PDBTitle: crystal structure of ancylostoma ceylanicum excretory-secretory2 protein 2 Phyre2 PDB 2r7t chain A Region: 25 - 48 Aligned: 21 Modelled: 24 Confidence: 8.6% Identity: 48% PDB header:transferase/rna Chain: A: PDB Molecule:rna-dependent rna polymerase; PDBTitle: crystal structure of rotavirus sa11 vp1/rna (ugugaacc)2 complex Phyre2 PDB 1jmu chain E Region: 22 - 29 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 63% PDB header:viral protein Chain: E: PDB Molecule:protein mu-1; PDBTitle: crystal structure of the reovirus mu1/sigma3 complex Phyre2 PDB 2i1t chain A Region: 74 - 84 Aligned: 11 Modelled: 11 Confidence: 5.5% Identity: 55% PDB header:toxin Chain: A: PDB Molecule:jingzhaotoxin-3; PDBTitle: solution structure of jingzhaotoxin-iii, a novel toxin2 inhibiting both nav and kv channels Phyre2 PDB 1yew chain I Region: 26 - 66 Aligned: 40 Modelled: 41 Confidence: 5.4% Identity: 33% PDB header:oxidoreductase, membrane protein Chain: I: PDB Molecule:particulate methane monooxygenase, b subunit; PDBTitle: crystal structure of particulate methane monooxygenase Phyre2 PDB 3rgb chain A Region: 26 - 66 Aligned: 40 Modelled: 41 Confidence: 5.4% Identity: 33% PDB header:oxidoreductase Chain: A: PDB Molecule:methane monooxygenase subunit b2; PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath) Phyre2 PDB 1kcw chain A Region: 50 - 86 Aligned: 33 Modelled: 37 Confidence: 5.3% Identity: 27% PDB header:oxidoreductase Chain: A: PDB Molecule:ceruloplasmin; PDBTitle: x-ray crystal structure of human ceruloplasmin at 3.0 angstroms Phyre2 1 d1sddb1 2 c1tvtA_ 3 d1mkfa_ 4 d1kqha_ 5 c3nswA_ 6 c2r7tA_ 7 c1jmuE_ 8 c2i1tA_ 9 c1yewI_ 10 c3rgbA_ 11 c1kcwA_

Detailed template information

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

1 d1sddb1 28.4 21 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Multidomain cupredoxins 2 c1tvtA_ 17.7 80 PDB header:transcription regulation Chain: A: PDB Molecule:transactivator protein; PDBTitle: structure of the equine infectious anemia virus tat protein 3 d1mkfa_ 17.1 22 Fold:Viral chemokine binding protein m3 Superfamily:Viral chemokine binding protein m3 Family:Viral chemokine binding protein m3 4 d1kqha_ 16.5 75 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins 5 c3nswA_ 9.0 45 PDB header:immune system Chain: A: PDB Molecule:excretory-secretory protein 2; PDBTitle: crystal structure of ancylostoma ceylanicum excretory-secretory2 protein 2 6 c2r7tA_ 8.6 48 PDB header:transferase/rna Chain: A: PDB Molecule:rna-dependent rna polymerase; PDBTitle: crystal structure of rotavirus sa11 vp1/rna (ugugaacc)2 complex 7 c1jmuE_ 5.6 63 PDB header:viral protein Chain: E: PDB Molecule:protein mu-1; PDBTitle: crystal structure of the reovirus mu1/sigma3 complex 8 c2i1tA_ 5.5 55 PDB header:toxin Chain: A: PDB Molecule:jingzhaotoxin-3; PDBTitle: solution structure of jingzhaotoxin-iii, a novel toxin2 inhibiting both nav and kv channels 9 c1yewI_ 5.4 33 PDB header:oxidoreductase, membrane protein Chain: I: PDB Molecule:particulate methane monooxygenase, b subunit; PDBTitle: crystal structure of particulate methane monooxygenase 10 c3rgbA_ 5.4 33 PDB header:oxidoreductase Chain: A: PDB Molecule:methane monooxygenase subunit b2; PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath) 11 c1kcwA_ 5.3 27 PDB header:oxidoreductase Chain: A: PDB Molecule:ceruloplasmin; PDBTitle: x-ray crystal structure of human ceruloplasmin at 3.0 angstroms

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