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

A

L

L

N

I

F

D

I

A

G

S

A

L

T

A

Q

S

Q

R

L

N

V

A

A

S

N

L

A

N

A

D

S

V

T

G

P

D

G

Q

P

Y

R

A

K

Q

V

V

F

Q

V

N

A

A

P

G

A

A

T

G

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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110

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120

Sequence

G

V

K

V

A

D

V

I

E

S

Q

A

P

D

K

L

V

Y

E

P

G

N

P

L

A

D

A

K

G

Y

V

K

M

P

N

V

D

V

V

G

E

M

V

N

T

M

S

A

S

R

S

Y

Q

A

N

V

E

V

L

N

Secondary structure

SS confidence

Disorder

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Disorder confidence

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130

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Sequence

T

V

K

S

M

M

L

K

T

L

T

L

G

Q

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 3a69 chain A Region: 6 - 133 Aligned: 118 Modelled: 118 Confidence: 99.9% Identity: 36% PDB header:motor protein Chain: A: PDB Molecule:flagellar hook protein flge; PDBTitle: atomic model of the bacterial flagellar hook based on2 docking an x-ray derived structure and terminal two alpha-3 helices into an 7.1 angstrom resolution cryoem map Phyre2 PDB 1ucu chain A Region: 87 - 134 Aligned: 48 Modelled: 48 Confidence: 94.9% Identity: 21% Fold: Phase 1 flagellin Superfamily: Phase 1 flagellin Family: Phase 1 flagellin Phyre2 PDB 1ory chain B Region: 95 - 134 Aligned: 40 Modelled: 39 Confidence: 83.4% Identity: 25% PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner Phyre2 PDB 3k8v chain B Region: 87 - 115 Aligned: 29 Modelled: 29 Confidence: 22.7% Identity: 21% PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 Phyre2 PDB 2b4j chain C domain 1 Region: 101 - 132 Aligned: 32 Modelled: 32 Confidence: 5.9% Identity: 16% Fold: N-cbl like Superfamily: HIV integrase-binding domain Family: HIV integrase-binding domain Phyre2 PDB 1z9e chain A Region: 101 - 132 Aligned: 32 Modelled: 32 Confidence: 5.6% Identity: 16% PDB header:protein binding/transcription Chain: A: PDB Molecule:pc4 and sfrs1 interacting protein 2; PDBTitle: solution structure of the hiv-1 integrase-binding domain in2 ledgf/p75 Phyre2 1 c3a69A_ 2 d1ucua_ 3 c1oryB_ 4 c3k8vB_ 5 d2b4jc1 6 c1z9eA_

Detailed template information

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

1 c3a69A_ 99.9 36 PDB header:motor protein Chain: A: PDB Molecule:flagellar hook protein flge; PDBTitle: atomic model of the bacterial flagellar hook based on2 docking an x-ray derived structure and terminal two alpha-3 helices into an 7.1 angstrom resolution cryoem map 2 d1ucua_ 94.9 21 Fold:Phase 1 flagellin Superfamily:Phase 1 flagellin Family:Phase 1 flagellin 3 c1oryB_ 83.4 25 PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner 4 c3k8vB_ 22.7 21 PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 5 d2b4jc1 5.9 16 Fold:N-cbl like Superfamily:HIV integrase-binding domain Family:HIV integrase-binding domain 6 c1z9eA_ 5.6 16 PDB header:protein binding/transcription Chain: A: PDB Molecule:pc4 and sfrs1 interacting protein 2; PDBTitle: solution structure of the hiv-1 integrase-binding domain in2 ledgf/p75

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