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

K

I

L

A

F

G

L

I

S

A

L

F

C

S

T

P

A

M

A

D

M

N

R

T

T

K

G

A

L

L

G

A

G

V

G

L

L

T

G

N

G

V

N

G

V

L

K

G

A

A

V

G

A

G

V

G

A

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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Sequence

V

T

E

K

G

R

D

G

K

N

A

R

K

G

A

K

V

G

A

A

V

G

A

V

T

G

V

L

T

G

N

G

L

E

G

A

I

K

G

A

V

I

G

G

T

G

G

A

I

L

G

K

M

K

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 1p42 chain A domain 1 Region: 23 - 58 Aligned: 36 Modelled: 36 Confidence: 14.8% Identity: 28% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC Phyre2 PDB 2go4 chain A Region: 23 - 58 Aligned: 36 Modelled: 36 Confidence: 11.2% Identity: 28% PDB header:hydrolase Chain: A: PDB Molecule:udp-3-o-[3-hydroxymyristoyl] n-acetylglucosamine PDBTitle: crystal structure of aquifex aeolicus lpxc complexed with tu-514 Phyre2 1 d1p42a1 2 c2go4A_

Detailed template information

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

1 d1p42a1 14.8 28 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC 2 c2go4A_ 11.2 28 PDB header:hydrolase Chain: A: PDB Molecule:udp-3-o-[3-hydroxymyristoyl] n-acetylglucosamine PDBTitle: crystal structure of aquifex aeolicus lpxc complexed with tu-514

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