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

R

K

R

K

S

R

N

N

S

K

I

G

H

G

A

I

S

R

I

G

R

P

N

N

P

F

E

P

C

R

N

R

Y

A

Q

K

Y

L

T

L

A

L

M

G

G

A

A

F

F

V

L

K

G

C

S

D

S

S

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

D

V

D

N

D

G

D

G

T

F

Y

A

T

V

Q

D

C

I

D

D

G

N

N

A

D

I

C

A

R

G

W

N

N

A

K

T

A

F

Y

A

D

V

P

K

N

M

T

Q

Q

N

C

Q

S

K

Y

E

N

C

Y

Y

Secondary structure

SS confidence

Disorder

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Disorder confidence

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130

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140

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150

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160

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170

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180

Sequence

D

N

V

E

Q

S

W

I

P

V

V

S

G

F

L

L

S

R

V

I

R

K

D

R

D

E

P

F

V

Y

N

S

G

G

S

S

F

A

S

R

P

V

W

R

S

T

S

G

D

Y

S

W

R

S

G

S

G

K

K

E

Secondary structure

SS confidence

Disorder

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Disorder confidence

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190

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200

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210

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.

Sequence

S

Y

S

S

G

G

F

T

T

K

K

A

S

T

V

S

R

G

G

Y

G

R

S

S

S

A

R

G

H

W

G

G

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 1j3b chain A domain 1 Region: 47 - 59 Aligned: 13 Modelled: 13 Confidence: 23.2% Identity: 38% Fold: PEP carboxykinase-like Superfamily: PEP carboxykinase-like Family: PEP carboxykinase C-terminal domain Phyre2 PDB 1i8n chain A Region: 63 - 79 Aligned: 17 Modelled: 17 Confidence: 16.7% Identity: 29% Fold: Hairpin loop containing domain-like Superfamily: Hairpin loop containing domain-like Family: Anti-platelet protein Phyre2 PDB 1i8n chain A Region: 63 - 79 Aligned: 17 Modelled: 17 Confidence: 16.7% Identity: 29% PDB header:toxin Chain: A: PDB Molecule:anti-platelet protein; PDBTitle: crystal structure of leech anti-platelet protein Phyre2 PDB 2lbg chain A Region: 131 - 141 Aligned: 11 Modelled: 11 Confidence: 15.3% Identity: 18% PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles Phyre2 PDB 1o0s chain A domain 1 Region: 36 - 93 Aligned: 54 Modelled: 58 Confidence: 11.8% Identity: 17% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Aminoacid dehydrogenase-like, C-terminal domain Phyre2 PDB 1yvy chain A Region: 47 - 59 Aligned: 13 Modelled: 13 Confidence: 11.0% Identity: 38% PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase [atp]; PDBTitle: crystal strucutre of anaerobiospirillum succiniciproducens2 phosphoenolpyruvate carboxykinase Phyre2 PDB 1gz3 chain B Region: 36 - 93 Aligned: 54 Modelled: 58 Confidence: 10.2% Identity: 13% PDB header:oxidoreductase Chain: B: PDB Molecule:nad-dependent malic enzyme; PDBTitle: molecular mechanism for the regulation of human mitochondrial2 nad(p)+-dependent malic enzyme by atp and fumarate Phyre2 PDB 3ehw chain A Region: 196 - 203 Aligned: 8 Modelled: 8 Confidence: 9.5% Identity: 63% PDB header:hydrolase Chain: A: PDB Molecule:dutp pyrophosphatase; PDBTitle: human dutpase in complex with alpha,beta-imido-dutp and mg2+:2 visualization of the full-length c-termini in all monomers and3 suggestion for an additional metal ion binding site Phyre2 PDB 1vji chain A Region: 133 - 154 Aligned: 22 Modelled: 22 Confidence: 8.4% Identity: 14% Fold: TIM beta/alpha-barrel Superfamily: FMN-linked oxidoreductases Family: FMN-linked oxidoreductases Phyre2 PDB 2aw5 chain A Region: 36 - 93 Aligned: 54 Modelled: 58 Confidence: 8.3% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:nadp-dependent malic enzyme; PDBTitle: crystal structure of a human malic enzyme Phyre2 PDB 1lj2 chain D Region: 30 - 39 Aligned: 10 Modelled: 10 Confidence: 7.9% Identity: 30% PDB header:viral protein/ translation Chain: D: PDB Molecule:eukaryotic protein synthesis initiation factor; PDBTitle: recognition of eif4g by rotavirus nsp3 reveals a basis for2 mrna circularization Phyre2 PDB 1gq2 chain A domain 1 Region: 36 - 93 Aligned: 54 Modelled: 58 Confidence: 7.9% Identity: 15% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Aminoacid dehydrogenase-like, C-terminal domain Phyre2 PDB 1o0s chain B Region: 36 - 93 Aligned: 54 Modelled: 58 Confidence: 7.8% Identity: 17% PDB header:oxidoreductase Chain: B: PDB Molecule:nad-dependent malic enzyme; PDBTitle: crystal structure of ascaris suum malic enzyme complexed with nadh Phyre2 PDB 1pj3 chain A domain 1 Region: 36 - 93 Aligned: 54 Modelled: 58 Confidence: 7.7% Identity: 13% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Aminoacid dehydrogenase-like, C-terminal domain Phyre2 PDB 2k7i chain A domain 1 Region: 162 - 191 Aligned: 30 Modelled: 30 Confidence: 7.5% Identity: 20% Fold: YegP-like Superfamily: YegP-like Family: YegP-like Phyre2 PDB 2k7i chain B Region: 162 - 191 Aligned: 30 Modelled: 30 Confidence: 7.5% Identity: 20% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:upf0339 protein atu0232; PDBTitle: solution nmr structure of protein atu0232 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att3. ontario center for structural proteomics target atc0223. Phyre2 PDB 1vyr chain A Region: 133 - 154 Aligned: 22 Modelled: 22 Confidence: 7.1% Identity: 18% Fold: TIM beta/alpha-barrel Superfamily: FMN-linked oxidoreductases Family: FMN-linked oxidoreductases Phyre2 PDB 1f7r chain A Region: 197 - 203 Aligned: 7 Modelled: 7 Confidence: 7.1% Identity: 71% Fold: beta-clip Superfamily: dUTPase-like Family: dUTPase-like Phyre2 PDB 3bid chain A domain 1 Region: 162 - 191 Aligned: 30 Modelled: 30 Confidence: 6.9% Identity: 27% Fold: YegP-like Superfamily: YegP-like Family: YegP-like Phyre2 PDB 1dos chain A Region: 51 - 106 Aligned: 46 Modelled: 56 Confidence: 6.2% Identity: 20% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: Class II FBP aldolase Phyre2 1 d1j3ba1 2 d1i8na_ 3 c1i8nA_ 4 c2lbgA_ 5 d1o0sa1 6 c1yvyA_ 7 c1gz3B_ 8 c3ehwA_ 9 d1vjia_ 10 c2aw5A_ 11 c1lj2D_ 12 d1gq2a1 13 c1o0sB_ 14 d1pj3a1 15 d2k7ia1 16 c2k7iB_ 17 d1vyra_ 18 d1f7ra_ 19 d3bida1 20 d1dosa_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 d1j3ba1 23.2 38 Fold:PEP carboxykinase-like Superfamily:PEP carboxykinase-like Family:PEP carboxykinase C-terminal domain 2 d1i8na_ 16.7 29 Fold:Hairpin loop containing domain-like Superfamily:Hairpin loop containing domain-like Family:Anti-platelet protein 3 c1i8nA_ 16.7 29 PDB header:toxin Chain: A: PDB Molecule:anti-platelet protein; PDBTitle: crystal structure of leech anti-platelet protein 4 c2lbgA_ 15.3 18 PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles 5 d1o0sa1 11.8 17 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain 6 c1yvyA_ 11.0 38 PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase [atp]; PDBTitle: crystal strucutre of anaerobiospirillum succiniciproducens2 phosphoenolpyruvate carboxykinase 7 c1gz3B_ 10.2 13 PDB header:oxidoreductase Chain: B: PDB Molecule:nad-dependent malic enzyme; PDBTitle: molecular mechanism for the regulation of human mitochondrial2 nad(p)+-dependent malic enzyme by atp and fumarate 8 c3ehwA_ 9.5 63 PDB header:hydrolase Chain: A: PDB Molecule:dutp pyrophosphatase; PDBTitle: human dutpase in complex with alpha,beta-imido-dutp and mg2+:2 visualization of the full-length c-termini in all monomers and3 suggestion for an additional metal ion binding site 9 d1vjia_ 8.4 14 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 10 c2aw5A_ 8.3 13 PDB header:oxidoreductase Chain: A: PDB Molecule:nadp-dependent malic enzyme; PDBTitle: crystal structure of a human malic enzyme 11 c1lj2D_ 7.9 30 PDB header:viral protein/ translation Chain: D: PDB Molecule:eukaryotic protein synthesis initiation factor; PDBTitle: recognition of eif4g by rotavirus nsp3 reveals a basis for2 mrna circularization 12 d1gq2a1 7.9 15 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain 13 c1o0sB_ 7.8 17 PDB header:oxidoreductase Chain: B: PDB Molecule:nad-dependent malic enzyme; PDBTitle: crystal structure of ascaris suum malic enzyme complexed with nadh 14 d1pj3a1 7.7 13 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain 15 d2k7ia1 7.5 20 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 16 c2k7iB_ 7.5 20 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:upf0339 protein atu0232; PDBTitle: solution nmr structure of protein atu0232 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att3. ontario center for structural proteomics target atc0223. 17 d1vyra_ 7.1 18 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 18 d1f7ra_ 7.1 71 Fold:beta-clip Superfamily:dUTPase-like Family:dUTPase-like 19 d3bida1 6.9 27 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 20 d1dosa_ 6.2 20 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class II FBP aldolase 21 c1qr6A_ not modelled 6.0 13 PDB header:oxidoreductase Chain: A: PDB Molecule:malic enzyme 2; PDBTitle: human mitochondrial nad(p)-dependent malic enzyme 22 d1oyaa_ not modelled 5.9 18 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 23 d1icpa_ not modelled 5.8 14 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 24 d1q45a_ not modelled 5.8 14 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 25 c3lyiA_ not modelled 5.6 6 PDB header:transcription Chain: A: PDB Molecule:bromodomain-containing protein 1; PDBTitle: pwwp domain of human bromodomain-containing protein 1 26 c3l5aA_ not modelled 5.4 5 PDB header:oxidoreductase Chain: A: PDB Molecule:nadh/flavin oxidoreductase/nadh oxidase; PDBTitle: crystal structure of a probable nadh-dependent flavin oxidoreductase2 from staphylococcus aureus 27 c1ylhA_ not modelled 5.3 38 PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase; PDBTitle: crystal structure of phosphoenolpyruvate carboxykinase from2 actinobaccilus succinogenes in complex with manganese and3 pyruvate 28 c2gq8A_ not modelled 5.2 18 PDB header:oxidoreductase Chain: A: PDB Molecule:oxidoreductase, fmn-binding; PDBTitle: structure of sye1, an oye homologue from s. ondeidensis, in complex2 with p-hydroxyacetophenone 29 d1z41a1 not modelled 5.2 14 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 30 c3gkaB_ not modelled 5.1 18 PDB header:oxidoreductase Chain: B: PDB Molecule:n-ethylmaleimide reductase; PDBTitle: crystal structure of n-ethylmaleimidine reductase from2 burkholderia pseudomallei

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