Secondary structure and disorder prediction

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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

K

V

L

Y

G

I

F

A

I

S

A

L

A

A

T

S

A

W

A

A

P

V

Q

V

G

E

A

A

G

S

A

A

T

S

V

S

A

G

S

S

S

A

T

S

V

S

T

V

S

S

A

V

G

V

A

L

A

A

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

Sequence

T

G

G

G

D

G

S

N

T

G

T

T

T

T

T

T

T

S

T

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 1h41 chain A domain 2 Region: 4 - 29 Aligned: 26 Modelled: 26 Confidence: 7.3% Identity: 31% Fold: Zincin-like Superfamily: beta-N-acetylhexosaminidase-like domain Family: alpha-D-glucuronidase, N-terminal domain Phyre2 PDB 1jug chain A Region: 6 - 12 Aligned: 7 Modelled: 7 Confidence: 5.6% Identity: 57% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: C-type lysozyme Phyre2 PDB 1gd6 chain A Region: 6 - 12 Aligned: 7 Modelled: 7 Confidence: 5.5% Identity: 57% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: C-type lysozyme Phyre2 PDB 1n13 chain J Region: 31 - 66 Aligned: 36 Modelled: 36 Confidence: 5.4% Identity: 22% PDB header:lyase Chain: J: PDB Molecule:pyruvoyl-dependent arginine decarboxylase alpha PDBTitle: the crystal structure of pyruvoyl-dependent arginine2 decarboxylase from methanococcus jannashii Phyre2 PDB 2vb1 chain A domain 1 Region: 6 - 12 Aligned: 7 Modelled: 7 Confidence: 5.4% Identity: 57% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: C-type lysozyme Phyre2 PDB 1yro chain A domain 1 Region: 6 - 12 Aligned: 7 Modelled: 7 Confidence: 5.3% Identity: 71% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: C-type lysozyme Phyre2 PDB 1ghl chain A Region: 6 - 12 Aligned: 7 Modelled: 7 Confidence: 5.3% Identity: 57% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: C-type lysozyme Phyre2 PDB 2goi chain C Region: 6 - 12 Aligned: 7 Modelled: 7 Confidence: 5.2% Identity: 71% PDB header:cell adhesion, sugar binding protein Chain: C: PDB Molecule:sperm lysozyme-like protein 1; PDBTitle: crystal structure of mouse sperm c-type lysozyme-like2 protein 1 Phyre2 1 d1h41a2 2 d1juga_ 3 d1gd6a_ 4 c1n13J_ 5 d2vb1a1 6 d1yroa1 7 d1ghla_ 8 c2goiC_

Detailed template information

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

1 d1h41a2 7.3 31 Fold:Zincin-like Superfamily:beta-N-acetylhexosaminidase-like domain Family:alpha-D-glucuronidase, N-terminal domain 2 d1juga_ 5.6 57 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 3 d1gd6a_ 5.5 57 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 4 c1n13J_ 5.4 22 PDB header:lyase Chain: J: PDB Molecule:pyruvoyl-dependent arginine decarboxylase alpha PDBTitle: the crystal structure of pyruvoyl-dependent arginine2 decarboxylase from methanococcus jannashii 5 d2vb1a1 5.4 57 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 6 d1yroa1 5.3 71 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 7 d1ghla_ 5.3 57 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 8 c2goiC_ 5.2 71 PDB header:cell adhesion, sugar binding protein Chain: C: PDB Molecule:sperm lysozyme-like protein 1; PDBTitle: crystal structure of mouse sperm c-type lysozyme-like2 protein 1

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