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

K

I

T

L

L

V

T

L

L

F

G

L

V

F

L

T

T

V

G

A

A

E

R

T

L

T

P

Q

Q

Q

R

M

T

S

C

N

Q

Q

A

T

A

Q

A

L

K

G

D

A

R

K

T

Y

M

S

D

C

L

K

N

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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100

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Sequence

S

K

S

A

P

G

E

K

S

L

T

P

Q

Q

Q

K

M

R

E

C

N

N

Q

A

T

Q

Q

S

L

K

G

D

D

R

N

K

F

M

S

A

C

L

K

K

A

A

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 1hek chain A Region: 43 - 53 Aligned: 11 Modelled: 11 Confidence: 13.5% Identity: 36% Fold: Retroviral matrix proteins Superfamily: Retroviral matrix proteins Family: EIAV matrix antigen Phyre2 PDB 3dwl chain E Region: 97 - 104 Aligned: 8 Modelled: 8 Confidence: 8.4% Identity: 50% PDB header:structural protein Chain: E: PDB Molecule:actin-related protein 2/3 complex subunit 3; PDBTitle: crystal structure of fission yeast arp2/3 complex lacking the arp22 subunit Phyre2 PDB 2bmf chain A domain 1 Region: 45 - 53 Aligned: 9 Modelled: 9 Confidence: 8.3% Identity: 67% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RNA helicase Phyre2 1 d1heka_ 2 c3dwlE_ 3 d2bmfa1

Detailed template information

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

1 d1heka_ 13.5 36 Fold:Retroviral matrix proteins Superfamily:Retroviral matrix proteins Family:EIAV matrix antigen 2 c3dwlE_ 8.4 50 PDB header:structural protein Chain: E: PDB Molecule:actin-related protein 2/3 complex subunit 3; PDBTitle: crystal structure of fission yeast arp2/3 complex lacking the arp22 subunit 3 d2bmfa1 8.3 67 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RNA helicase

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