Secondary structure and disorder prediction

1

.

.

.

.

.

.

.

.

10

.

.

.

.

.

.

.

.

.

20

.

.

.

.

.

.

.

.

.

30

.

.

.

.

.

.

.

.

.

40

.

.

.

.

.

.

.

.

.

50

.

.

.

.

.

.

.

.

.

60

Sequence

M

L

A

L

M

D

A

D

G

N

I

A

W

S

G

E

Y

D

E

W

G

N

Q

L

N

E

E

N

P

H

H

L

H

Q

P

Y

R

L

P

G

Q

Q

Y

D

K

E

S

G

L

Y

Y

N

R

N

R

Y

Y

D

P

L

Secondary structure

SS confidence

Disorder

?

?

?

?

?

Disorder confidence

.

.

.

.

.

.

.

.

.

70

.

.

.

.

.

.

.

.

.

80

.

.

.

.

.

.

.

.

.

90

.

.

.

.

.

.

.

.

.

100

.

.

.

.

.

.

.

.

.

110

.

.

.

.

.

.

.

.

.

120

Sequence

Q

G

R

Y

I

T

Q

D

P

I

G

L

E

G

G

W

S

L

Y

A

Y

P

L

N

P

V

N

G

I

D

P

L

G

L

S

P

A

D

V

A

L

I

R

R

K

D

Q

L

N

H

Q

R

A

W

D

I

L

S

D

T

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

.

.

.

.

.

.

.

.

.

130

.

.

.

.

.

.

.

.

.

140

.

.

.

.

.

.

.

.

.

150

.

.

.

.

.

.

.

.

.

160

.

.

.

.

.

.

.

.

.

170

.

.

.

.

.

.

.

.

.

180

Sequence

Y

E

D

M

K

R

L

N

L

G

G

T

D

Q

F

F

H

C

M

A

F

C

R

V

S

K

L

N

D

A

G

V

S

R

S

A

K

G

L

G

Y

E

K

E

I

R

D

Y

G

L

N

L

F

G

M

Y

G

R

K

V

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

.

.

.

.

.

.

.

.

.

190

.

.

.

.

.

.

.

.

.

200

.

.

.

.

.

.

.

.

.

210

.

.

.

.

.

.

.

.

.

220

.

.

.

.

.

.

.

.

.

230

.

.

.

.

.

.

Sequence

K

L

S

H

S

E

M

I

E

D

N

K

K

D

L

A

V

N

D

H

G

L

T

C

P

S

T

T

D

C

S

D

R

C

S

D

Y

I

N

P

E

H

K

K

T

I

K

A

L

Q

D

A

G

Y

L

K

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 1x3z chain A domain 1 Region: 56 - 89 Aligned: 34 Modelled: 34 Confidence: 18.3% Identity: 12% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Transglutaminase core Phyre2 PDB 2f4m chain A domain 1 Region: 56 - 89 Aligned: 34 Modelled: 34 Confidence: 13.2% Identity: 24% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Transglutaminase core Phyre2 PDB 1c3h chain A Region: 57 - 69 Aligned: 13 Modelled: 13 Confidence: 7.6% Identity: 31% Fold: TNF-like Superfamily: TNF-like Family: TNF-like Phyre2 PDB 3m1h chain B Region: 38 - 70 Aligned: 33 Modelled: 33 Confidence: 6.5% Identity: 15% PDB header:cell invasion Chain: B: PDB Molecule:lysine specific cysteine protease; PDBTitle: crystal structure analysis of the k3 cleaved adhesin domain of lys-2 gingipain (kgp) from porphyromonas gingivalis w83 Phyre2 PDB 3esw chain A Region: 56 - 69 Aligned: 14 Modelled: 14 Confidence: 5.8% Identity: 21% PDB header:hydrolase Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine PDBTitle: complex of yeast pngase with glcnac2-iac. Phyre2 PDB 2ka3 chain C Region: 57 - 69 Aligned: 13 Modelled: 13 Confidence: 5.7% Identity: 31% PDB header:structural protein Chain: C: PDB Molecule:emilin-1; PDBTitle: structure of emilin-1 c1q-like domain Phyre2 PDB 1zak chain A domain 2 Region: 40 - 51 Aligned: 12 Modelled: 12 Confidence: 5.6% Identity: 33% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1m3y chain A domain 2 Region: 75 - 93 Aligned: 18 Modelled: 19 Confidence: 5.6% Identity: 39% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Group II dsDNA viruses VP Family: Major capsid protein vp54 Phyre2 PDB 1bco chain A domain 1 Region: 48 - 65 Aligned: 18 Modelled: 18 Confidence: 5.1% Identity: 22% Fold: mu transposase, C-terminal domain Superfamily: mu transposase, C-terminal domain Family: mu transposase, C-terminal domain Phyre2 1 d1x3za1 2 d2f4ma1 3 d1c3ha_ 4 c3m1hB_ 5 c3eswA_ 6 c2ka3C_ 7 d1zaka2 8 d1m3ya2 9 d1bcoa1

Detailed template information

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

1 d1x3za1 18.3 12 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 2 d2f4ma1 13.2 24 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 3 d1c3ha_ 7.6 31 Fold:TNF-like Superfamily:TNF-like Family:TNF-like 4 c3m1hB_ 6.5 15 PDB header:cell invasion Chain: B: PDB Molecule:lysine specific cysteine protease; PDBTitle: crystal structure analysis of the k3 cleaved adhesin domain of lys-2 gingipain (kgp) from porphyromonas gingivalis w83 5 c3eswA_ 5.8 21 PDB header:hydrolase Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine PDBTitle: complex of yeast pngase with glcnac2-iac. 6 c2ka3C_ 5.7 31 PDB header:structural protein Chain: C: PDB Molecule:emilin-1; PDBTitle: structure of emilin-1 c1q-like domain 7 d1zaka2 5.6 33 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 8 d1m3ya2 5.6 39 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Major capsid protein vp54 9 d1bcoa1 5.1 22 Fold:mu transposase, C-terminal domain Superfamily:mu transposase, C-terminal domain Family:mu transposase, C-terminal domain

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