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

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R

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L

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P

D

V

V

G

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D

A

L

V

H

D

H

Q

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V

L

A

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A

E

G

G

V

V

A

V

F

A

N

N

A

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A

F

Y

A

V

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P

A

R

L

A

E

L

L

A

L

E

E

K

L

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

A

R

P

G

S

D

V

A

L

D

D

Q

L

Y

Q

E

P

Q

A

A

P

V

A

V

P

M

G

K

F

A

M

Y

P

D

W

Q

P

D

A

D

F

I

R

L

A

A

L

W

G

V

A

L

R

E

P

V

T

T

E

E

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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Sequence

L

A

S

F

I

A

Y

W

Q

A

E

G

K

V

F

H

H

V

Q

W

Q

Q

K

L

A

R

S

L

Q

I

G

R

A

S

N

G

G

L

P

K

R

D

V

N

T

V

S

E

P

D

S

Q

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P

P

G

F

R

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 3bjq chain A Region: 10 - 58 Aligned: 35 Modelled: 48 Confidence: 25.0% Identity: 23% PDB header:viral protein Chain: A: PDB Molecule:phage-related protein; PDBTitle: crystal structure of a phage-related protein (bb3626) from bordetella2 bronchiseptica rb50 at 2.05 a resolution Phyre2 PDB 2e52 chain A Region: 123 - 160 Aligned: 38 Modelled: 38 Confidence: 20.4% Identity: 26% PDB header:hydrolase/dna Chain: A: PDB Molecule:type ii restriction enzyme hindiii; PDBTitle: crystal structural analysis of hindiii restriction endonuclease in2 complex with cognate dna at 2.0 angstrom resolution Phyre2 PDB 1m9z chain A Region: 9 - 25 Aligned: 17 Modelled: 17 Confidence: 18.2% Identity: 12% Fold: Snake toxin-like Superfamily: Snake toxin-like Family: Extracellular domain of cell surface receptors Phyre2 PDB 1ks6 chain A Region: 9 - 25 Aligned: 17 Modelled: 17 Confidence: 18.0% Identity: 29% Fold: Snake toxin-like Superfamily: Snake toxin-like Family: Extracellular domain of cell surface receptors Phyre2 PDB 2pjy chain B domain 1 Region: 9 - 25 Aligned: 17 Modelled: 17 Confidence: 17.7% Identity: 12% Fold: Snake toxin-like Superfamily: Snake toxin-like Family: Extracellular domain of cell surface receptors Phyre2 PDB 1plo chain A Region: 9 - 25 Aligned: 17 Modelled: 17 Confidence: 16.7% Identity: 12% Fold: Snake toxin-like Superfamily: Snake toxin-like Family: Extracellular domain of cell surface receptors Phyre2 PDB 2kgm chain A Region: 129 - 156 Aligned: 22 Modelled: 28 Confidence: 14.9% Identity: 41% PDB header:signaling protein Chain: A: PDB Molecule:protein ste5; PDBTitle: solution structure of ste5pm24 in sds micelle Phyre2 PDB 2l4u chain A Region: 129 - 156 Aligned: 22 Modelled: 28 Confidence: 11.8% Identity: 41% PDB header:signaling protein Chain: A: PDB Molecule:24mer peptide from protein ste5; PDBTitle: solution structure of ste5pm24 in the presence of sds micelle Phyre2 PDB 1xk5 chain A Region: 122 - 129 Aligned: 8 Modelled: 8 Confidence: 9.3% Identity: 38% PDB header:transport protein Chain: A: PDB Molecule:snurportin-1; PDBTitle: crystal structure of the m3g-cap-binding domain of2 snurportin1 in complex with a m3gpppg-cap dinucleotide Phyre2 PDB 1ukf chain A Region: 21 - 68 Aligned: 47 Modelled: 48 Confidence: 9.0% Identity: 19% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Avirulence protein Avrpph3 Phyre2 PDB 2fcw chain A domain 1 Region: 102 - 126 Aligned: 25 Modelled: 25 Confidence: 8.9% Identity: 32% Fold: RAP domain-like Superfamily: RAP domain-like Family: RAP domain Phyre2 PDB 3gb8 chain B Region: 122 - 129 Aligned: 8 Modelled: 8 Confidence: 8.0% Identity: 38% PDB header:transport protein Chain: B: PDB Molecule:snurportin-1; PDBTitle: crystal structure of crm1/snurportin-1 complex Phyre2 PDB 3gjx chain E Region: 122 - 129 Aligned: 8 Modelled: 8 Confidence: 7.6% Identity: 38% PDB header:protein transport Chain: E: PDB Molecule:snurportin-1; PDBTitle: crystal structure of the nuclear export complex crm1-2 snurportin1-rangtp Phyre2 PDB 3h7h chain A Region: 30 - 46 Aligned: 17 Modelled: 17 Confidence: 7.3% Identity: 41% PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt4; PDBTitle: crystal structure of the human transcription elongation factor dsif,2 hspt4/hspt5 (176-273) Phyre2 PDB 2zxr chain A Region: 5 - 23 Aligned: 18 Modelled: 19 Confidence: 6.3% Identity: 44% PDB header:hydrolase Chain: A: PDB Molecule:single-stranded dna specific exonuclease recj; PDBTitle: crystal structure of recj in complex with mg2+ from thermus2 thermophilus hb8 Phyre2 PDB 2fok chain A domain 1 Region: 26 - 85 Aligned: 50 Modelled: 60 Confidence: 6.2% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Restriction endonuclease FokI, N-terminal (recognition) domain Phyre2 PDB 1txk chain A Region: 109 - 133 Aligned: 25 Modelled: 25 Confidence: 6.2% Identity: 28% PDB header:biosynthetic protein Chain: A: PDB Molecule:glucans biosynthesis protein g; PDBTitle: crystal structure of escherichia coli opgg Phyre2 PDB 1f44 chain A domain 1 Region: 99 - 132 Aligned: 33 Modelled: 34 Confidence: 6.1% Identity: 21% Fold: SAM domain-like Superfamily: lambda integrase-like, N-terminal domain Family: lambda integrase-like, N-terminal domain Phyre2 PDB 1j0s chain A Region: 5 - 46 Aligned: 42 Modelled: 42 Confidence: 6.1% Identity: 12% Fold: beta-Trefoil Superfamily: Cytokine Family: Interleukin-1 (IL-1) Phyre2 PDB 1txk chain A domain 2 Region: 109 - 133 Aligned: 25 Modelled: 25 Confidence: 6.1% Identity: 28% Fold: Supersandwich Superfamily: Galactose mutarotase-like Family: MdoG-like Phyre2 1 c3bjqA_ 2 c2e52A_ 3 d1m9za_ 4 d1ks6a_ 5 d2pjyb1 6 d1ploa_ 7 c2kgmA_ 8 c2l4uA_ 9 c1xk5A_ 10 d1ukfa_ 11 d2fcwa1 12 c3gb8B_ 13 c3gjxE_ 14 c3h7hA_ 15 c2zxrA_ 16 d2foka1 17 c1txkA_ 18 d1f44a1 19 d1j0sa_ 20 d1txka2 21 22 23

Detailed template information

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

1 c3bjqA_ 25.0 23 PDB header:viral protein Chain: A: PDB Molecule:phage-related protein; PDBTitle: crystal structure of a phage-related protein (bb3626) from bordetella2 bronchiseptica rb50 at 2.05 a resolution 2 c2e52A_ 20.4 26 PDB header:hydrolase/dna Chain: A: PDB Molecule:type ii restriction enzyme hindiii; PDBTitle: crystal structural analysis of hindiii restriction endonuclease in2 complex with cognate dna at 2.0 angstrom resolution 3 d1m9za_ 18.2 12 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors 4 d1ks6a_ 18.0 29 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors 5 d2pjyb1 17.7 12 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors 6 d1ploa_ 16.7 12 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors 7 c2kgmA_ 14.9 41 PDB header:signaling protein Chain: A: PDB Molecule:protein ste5; PDBTitle: solution structure of ste5pm24 in sds micelle 8 c2l4uA_ 11.8 41 PDB header:signaling protein Chain: A: PDB Molecule:24mer peptide from protein ste5; PDBTitle: solution structure of ste5pm24 in the presence of sds micelle 9 c1xk5A_ 9.3 38 PDB header:transport protein Chain: A: PDB Molecule:snurportin-1; PDBTitle: crystal structure of the m3g-cap-binding domain of2 snurportin1 in complex with a m3gpppg-cap dinucleotide 10 d1ukfa_ 9.0 19 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Avirulence protein Avrpph3 11 d2fcwa1 8.9 32 Fold:RAP domain-like Superfamily:RAP domain-like Family:RAP domain 12 c3gb8B_ 8.0 38 PDB header:transport protein Chain: B: PDB Molecule:snurportin-1; PDBTitle: crystal structure of crm1/snurportin-1 complex 13 c3gjxE_ 7.6 38 PDB header:protein transport Chain: E: PDB Molecule:snurportin-1; PDBTitle: crystal structure of the nuclear export complex crm1-2 snurportin1-rangtp 14 c3h7hA_ 7.3 41 PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt4; PDBTitle: crystal structure of the human transcription elongation factor dsif,2 hspt4/hspt5 (176-273) 15 c2zxrA_ 6.3 44 PDB header:hydrolase Chain: A: PDB Molecule:single-stranded dna specific exonuclease recj; PDBTitle: crystal structure of recj in complex with mg2+ from thermus2 thermophilus hb8 16 d2foka1 6.2 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Restriction endonuclease FokI, N-terminal (recognition) domain 17 c1txkA_ 6.2 28 PDB header:biosynthetic protein Chain: A: PDB Molecule:glucans biosynthesis protein g; PDBTitle: crystal structure of escherichia coli opgg 18 d1f44a1 6.1 21 Fold:SAM domain-like Superfamily:lambda integrase-like, N-terminal domain Family:lambda integrase-like, N-terminal domain 19 d1j0sa_ 6.1 12 Fold:beta-Trefoil Superfamily:Cytokine Family:Interleukin-1 (IL-1) 20 d1txka2 6.1 28 Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:MdoG-like 21 d2ftua1 not modelled 6.0 32 Fold:RAP domain-like Superfamily:RAP domain-like Family:RAP domain 22 c2kgnA_ not modelled 6.0 41 PDB header:signaling protein Chain: A: PDB Molecule:protein ste5; PDBTitle: solution structure of ste5pm24 in the zwitterionic dpc2 micelle 23 c2hyiJ_ not modelled 5.7 29 PDB header:hydrolase/rna binding protein/rna Chain: J: PDB Molecule:protein casc3; PDBTitle: structure of the human exon junction complex with a trapped2 dead-box helicase bound to rna

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