Secondary structure and disorder prediction

1

.

.

.

.

.

.

.

.

10

.

.

.

.

.

.

.

.

.

20

.

.

.

.

.

.

.

.

.

30

.

.

.

.

.

.

.

.

.

40

.

.

.

.

.

.

.

.

.

50

.

.

.

.

.

.

.

.

.

60

Sequence

M

C

P

E

C

F

F

L

M

L

F

F

C

G

Y

R

A

C

Y

C

S

S

S

F

S

S

S

S

S

S

S

S

S

S

S

F

R

S

S

P

A

Y

G

F

S

G

R

P

P

G

G

A

G

C

R

E

R

S

Q

R

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

.

.

.

.

.

.

.

.

.

70

.

.

.

.

.

.

.

.

.

80

.

.

.

.

.

.

.

.

.

90

.

.

.

.

.

.

.

.

.

100

.

.

.

.

.

.

.

.

.

110

.

.

.

.

.

.

.

.

.

120

Sequence

S

C

L

R

P

G

G

L

P

S

L

T

R

N

P

G

L

Q

R

P

F

R

S

R

R

L

C

R

A

V

A

C

A

P

G

I

P

A

K

G

R

R

D

V

R

G

N

A

V

S

Q

T

A

L

H

V

V

A

A

G

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

.

.

.

.

.

.

.

.

.

130

.

.

Sequence

P

C

S

L

P

A

G

C

H

T

P

V

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

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 2l61 chain A Region: 49 - 60 Aligned: 12 Modelled: 12 Confidence: 20.9% Identity: 67% PDB header:metal binding protein Chain: A: PDB Molecule:ec protein i/ii; PDBTitle: protein and metal cluster structure of the wheat metallothionein2 domain g-ec-1. the second part of the puzzle. Phyre2 PDB 3ush chain B Region: 15 - 54 Aligned: 40 Modelled: 40 Confidence: 8.1% Identity: 28% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the q2s0r5 protein from salinibacter ruber,2 northeast structural genomics consortium target srr207 Phyre2 PDB 2l53 chain B Region: 77 - 93 Aligned: 17 Modelled: 17 Confidence: 8.1% Identity: 41% PDB header:ca-binding protein/proton transport Chain: B: PDB Molecule:voltage-gated sodium channel type v alpha isoform b PDBTitle: solution nmr structure of apo-calmodulin in complex with the iq motif2 of human cardiac sodium channel nav1.5 Phyre2 PDB 1id3 chain B Region: 40 - 46 Aligned: 7 Modelled: 7 Confidence: 6.5% Identity: 57% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 1 c2l61A_ 2 c3ushB_ 3 c2l53B_ 4 d1id3b_

Detailed template information

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

1 c2l61A_ 20.9 67 PDB header:metal binding protein Chain: A: PDB Molecule:ec protein i/ii; PDBTitle: protein and metal cluster structure of the wheat metallothionein2 domain g-ec-1. the second part of the puzzle. 2 c3ushB_ 8.1 28 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the q2s0r5 protein from salinibacter ruber,2 northeast structural genomics consortium target srr207 3 c2l53B_ 8.1 41 PDB header:ca-binding protein/proton transport Chain: B: PDB Molecule:voltage-gated sodium channel type v alpha isoform b PDBTitle: solution nmr structure of apo-calmodulin in complex with the iq motif2 of human cardiac sodium channel nav1.5 4 d1id3b_ 6.5 57 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones

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

---

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