Secondary structure and disorder prediction

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20

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40

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50

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60

Sequence

M

K

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L

R

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G

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A

P

C

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P

V

A

F

C

R

D

A

G

S

A

G

H

G

A

T

E

A

A

R

P

E

R

S

L

Q

A

R

G

F

A

S

G

M

E

A

R

Q

G

G

D

N

F

A

G

S

V

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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90

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100

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Sequence

H

D

S

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P

A

R

G

D

A

R

K

R

H

C

Q

E

N

N

K

T

D

R

N

Q

G

S

S

N

Q

S

Q

N

R

R

K

K

R

I

I

K

G

K

V

M

Secondary structure

SS confidence

Disorder

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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 1jma chain B domain 2 Region: 7 - 18 Aligned: 12 Modelled: 12 Confidence: 14.6% Identity: 50% Fold: TNF receptor-like Superfamily: TNF receptor-like Family: TNF receptor-like Phyre2 PDB 1y88 chain A domain 1 Region: 16 - 25 Aligned: 10 Modelled: 10 Confidence: 9.0% Identity: 70% Fold: SAM domain-like Superfamily: Rad51 N-terminal domain-like Family: Hypothetical protein AF1548, C-terminal domain Phyre2 PDB 1dfw chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 5.8% Identity: 43% PDB header:immune system Chain: A: PDB Molecule:lung surfactant protein b; PDBTitle: conformational mapping of the n-terminal segment of2 surfactant protein b in lipid using 13c-enhanced fourier3 transform infrared spectroscopy (ftir) Phyre2 1 d1jmab2 2 d1y88a1 3 c1dfwA_

Detailed template information

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

1 d1jmab2 14.6 50 Fold:TNF receptor-like Superfamily:TNF receptor-like Family:TNF receptor-like 2 d1y88a1 9.0 70 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:Hypothetical protein AF1548, C-terminal domain 3 c1dfwA_ 5.8 43 PDB header:immune system Chain: A: PDB Molecule:lung surfactant protein b; PDBTitle: conformational mapping of the n-terminal segment of2 surfactant protein b in lipid using 13c-enhanced fourier3 transform infrared spectroscopy (ftir)

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