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

F

R

S

L

F

L

A

A

A

L

M

A

F

T

P

L

A

A

N

A

G

E

I

T

L

L

P

S

I

K

L

Q

I

G

D

R

D

H

Y

G

N

Y

W

D

G

G

H

W

R

D

R

D

Y

W

H

R

N

Y

E

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

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

W

R

K

N

R

W

W

R

H

D

N

G

Y

H

R

G

W

D

K

R

K

A

Y

E

R

G

Y

R

E

G

W

R

D

R

D

D

H

R

G

K

G

R

G

H

G

H

R

H

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

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?

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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 1kf6 chain C Region: 68 - 87 Aligned: 20 Modelled: 20 Confidence: 20.4% Identity: 20% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1bvp chain 1 domain 2 Region: 18 - 38 Aligned: 21 Modelled: 21 Confidence: 12.7% Identity: 14% Fold: Viral protein domain Superfamily: Viral protein domain Family: Top domain of virus capsid protein Phyre2 PDB 2de0 chain X Region: 18 - 47 Aligned: 25 Modelled: 30 Confidence: 11.2% Identity: 40% PDB header:transferase Chain: X: PDB Molecule:alpha-(1,6)-fucosyltransferase; PDBTitle: crystal structure of human alpha 1,6-fucosyltransferase, fut8 Phyre2 PDB 1ahs chain A Region: 18 - 35 Aligned: 18 Modelled: 18 Confidence: 9.8% Identity: 6% Fold: Viral protein domain Superfamily: Viral protein domain Family: Top domain of virus capsid protein Phyre2 PDB 3kwp chain A Region: 4 - 31 Aligned: 28 Modelled: 28 Confidence: 9.6% Identity: 7% PDB header:transferase Chain: A: PDB Molecule:predicted methyltransferase; PDBTitle: crystal structure of putative methyltransferase from lactobacillus2 brevis Phyre2 PDB 1wj2 chain A Region: 45 - 50 Aligned: 6 Modelled: 6 Confidence: 9.4% Identity: 67% Fold: WRKY DNA-binding domain Superfamily: WRKY DNA-binding domain Family: WRKY DNA-binding domain Phyre2 PDB 2pq4 chain B Region: 10 - 30 Aligned: 21 Modelled: 21 Confidence: 9.2% Identity: 29% PDB header:chaperone/oxidoreductase Chain: B: PDB Molecule:periplasmic nitrate reductase precursor; PDBTitle: nmr solution structure of napd in complex with napa1-352 signal peptide Phyre2 PDB 1h3g chain A domain 1 Region: 20 - 43 Aligned: 24 Modelled: 23 Confidence: 9.0% Identity: 29% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: E-set domains of sugar-utilizing enzymes Phyre2 PDB 2fpe chain B Region: 18 - 44 Aligned: 27 Modelled: 27 Confidence: 8.5% Identity: 15% PDB header:signaling protein Chain: B: PDB Molecule:c-jun-amino-terminal kinase interacting protein PDBTitle: conserved dimerization of the ib1 src-homology 3 domain Phyre2 PDB 2zom chain C Region: 21 - 46 Aligned: 18 Modelled: 26 Confidence: 6.9% Identity: 28% PDB header:unknown function Chain: C: PDB Molecule:protein cuta, chloroplast, putative, expressed; PDBTitle: crystal structure of cuta1 from oryza sativa Phyre2 PDB 2ayd chain A Region: 45 - 50 Aligned: 6 Modelled: 6 Confidence: 6.8% Identity: 67% PDB header:transcription Chain: A: PDB Molecule:wrky transcription factor 1; PDBTitle: crystal structure of the c-terminal wrky domainof atwrky1,2 an sa-induced and partially npr1-dependent transcription3 factor Phyre2 PDB 1s4d chain A Region: 4 - 31 Aligned: 28 Modelled: 28 Confidence: 5.9% Identity: 11% Fold: Tetrapyrrole methylase Superfamily: Tetrapyrrole methylase Family: Tetrapyrrole methylase Phyre2 PDB 3m3w chain A Region: 41 - 48 Aligned: 8 Modelled: 8 Confidence: 5.5% Identity: 25% PDB header:endocytosis Chain: A: PDB Molecule:protein kinase c and casein kinase ii substrate protein 3; PDBTitle: crystal strcuture of mouse pacsin3 bar domain mutant Phyre2 1 d1kf6c_ 2 d1bvp12 3 c2de0X_ 4 d1ahsa_ 5 c3kwpA_ 6 d1wj2a_ 7 c2pq4B_ 8 d1h3ga1 9 c2fpeB_ 10 c2zomC_ 11 c2aydA_ 12 d1s4da_ 13 c3m3wA_

Detailed template information

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

1 d1kf6c_ 20.4 20 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 2 d1bvp12 12.7 14 Fold:Viral protein domain Superfamily:Viral protein domain Family:Top domain of virus capsid protein 3 c2de0X_ 11.2 40 PDB header:transferase Chain: X: PDB Molecule:alpha-(1,6)-fucosyltransferase; PDBTitle: crystal structure of human alpha 1,6-fucosyltransferase, fut8 4 d1ahsa_ 9.8 6 Fold:Viral protein domain Superfamily:Viral protein domain Family:Top domain of virus capsid protein 5 c3kwpA_ 9.6 7 PDB header:transferase Chain: A: PDB Molecule:predicted methyltransferase; PDBTitle: crystal structure of putative methyltransferase from lactobacillus2 brevis 6 d1wj2a_ 9.4 67 Fold:WRKY DNA-binding domain Superfamily:WRKY DNA-binding domain Family:WRKY DNA-binding domain 7 c2pq4B_ 9.2 29 PDB header:chaperone/oxidoreductase Chain: B: PDB Molecule:periplasmic nitrate reductase precursor; PDBTitle: nmr solution structure of napd in complex with napa1-352 signal peptide 8 d1h3ga1 9.0 29 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:E-set domains of sugar-utilizing enzymes 9 c2fpeB_ 8.5 15 PDB header:signaling protein Chain: B: PDB Molecule:c-jun-amino-terminal kinase interacting protein PDBTitle: conserved dimerization of the ib1 src-homology 3 domain 10 c2zomC_ 6.9 28 PDB header:unknown function Chain: C: PDB Molecule:protein cuta, chloroplast, putative, expressed; PDBTitle: crystal structure of cuta1 from oryza sativa 11 c2aydA_ 6.8 67 PDB header:transcription Chain: A: PDB Molecule:wrky transcription factor 1; PDBTitle: crystal structure of the c-terminal wrky domainof atwrky1,2 an sa-induced and partially npr1-dependent transcription3 factor 12 d1s4da_ 5.9 11 Fold:Tetrapyrrole methylase Superfamily:Tetrapyrrole methylase Family:Tetrapyrrole methylase 13 c3m3wA_ 5.5 25 PDB header:endocytosis Chain: A: PDB Molecule:protein kinase c and casein kinase ii substrate protein 3; PDBTitle: crystal strcuture of mouse pacsin3 bar domain mutant

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