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

V

N

A

A

Q

R

T

R

V

K

V

E

A

D

N

R

P

S

V

D

T

H

P

P

G

V

Q

P

S

P

G

T

G

G

T

R

H

H

N

F

M

L

C

V

V

L

A

V

P

V

F

S

L

V

L

S

G

T

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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Sequence

L

F

T

K

Q

R

R

V

S

P

D

D

G

L

I

T

R

P

I

L

I

A

V

A

T

G

A

L

L

C

F

V

E

K

L

T

D

R

A

G

S

I

C

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 2iur chain D Region: 19 - 31 Aligned: 13 Modelled: 13 Confidence: 9.9% Identity: 54% PDB header:oxidoreductase Chain: D: PDB Molecule:aromatic amine dehydrogenase beta subunit; PDBTitle: crystal structure of n-quinol form of aromatic amine2 dehydrogenase (aadh) from alcaligenes faecalis, form a3 cocrystal Phyre2 PDB 2awi chain A domain 1 Region: 11 - 18 Aligned: 8 Modelled: 8 Confidence: 9.0% Identity: 88% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: PrgX N-terminal domain-like Phyre2 PDB 1prt chain C domain 2 Region: 54 - 65 Aligned: 12 Modelled: 12 Confidence: 7.4% Identity: 50% Fold: C-type lectin-like Superfamily: C-type lectin-like Family: Aerolysin/Pertussis toxin (APT) domain Phyre2 PDB 1mda chain L Region: 19 - 36 Aligned: 18 Modelled: 18 Confidence: 6.2% Identity: 33% Fold: Methylamine dehydrogenase, L chain Superfamily: Methylamine dehydrogenase, L chain Family: Methylamine dehydrogenase, L chain Phyre2 PDB 3c75 chain L Region: 19 - 36 Aligned: 18 Modelled: 18 Confidence: 5.5% Identity: 22% PDB header:oxidoreductase Chain: L: PDB Molecule:methylamine dehydrogenase light chain; PDBTitle: paracoccus versutus methylamine dehydrogenase in complex2 with amicyanin Phyre2 PDB 1w36 chain B domain 1 Region: 27 - 84 Aligned: 50 Modelled: 58 Confidence: 5.5% Identity: 26% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Tandem AAA-ATPase domain Phyre2 PDB 2bbk chain L Region: 19 - 36 Aligned: 18 Modelled: 18 Confidence: 5.5% Identity: 22% Fold: Methylamine dehydrogenase, L chain Superfamily: Methylamine dehydrogenase, L chain Family: Methylamine dehydrogenase, L chain Phyre2 1 c2iurD_ 2 d2awia1 3 d1prtc2 4 d1mdal_ 5 c3c75L_ 6 d1w36b1 7 d2bbkl_

Detailed template information

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

1 c2iurD_ 9.9 54 PDB header:oxidoreductase Chain: D: PDB Molecule:aromatic amine dehydrogenase beta subunit; PDBTitle: crystal structure of n-quinol form of aromatic amine2 dehydrogenase (aadh) from alcaligenes faecalis, form a3 cocrystal 2 d2awia1 9.0 88 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:PrgX N-terminal domain-like 3 d1prtc2 7.4 50 Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Aerolysin/Pertussis toxin (APT) domain 4 d1mdal_ 6.2 33 Fold:Methylamine dehydrogenase, L chain Superfamily:Methylamine dehydrogenase, L chain Family:Methylamine dehydrogenase, L chain 5 c3c75L_ 5.5 22 PDB header:oxidoreductase Chain: L: PDB Molecule:methylamine dehydrogenase light chain; PDBTitle: paracoccus versutus methylamine dehydrogenase in complex2 with amicyanin 6 d1w36b1 5.5 26 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Tandem AAA-ATPase domain 7 d2bbkl_ 5.5 22 Fold:Methylamine dehydrogenase, L chain Superfamily:Methylamine dehydrogenase, L chain Family:Methylamine dehydrogenase, L chain

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