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

K

K

K

V

L

A

I

A

L

V

T

V

F

T

G

M

G

V

A

Q

A

A

D

V

T

A

Q

A

V

A

T

W

S

A

T

A

K

K

D

T

T

S

K

L

V

V

T

P

L

G

S

L

A

F

Q

Y

A

E

G

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

I

K

G

F

N

S

Q

K

G

L

F

D

V

A

I

E

G

D

S

T

A

T

A

F

K

L

T

S

R

L

I

T

N

T

L

T

Q

L

D

T

S

G

S

T

L

N

V

G

V

D

Y

N

G

A

A

V

E

K

T

G

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

T

V

M

I

D

T

A

N

G

V

L

G

G

N

L

S

P

L

A

N

G

Y

N

A

S

N

R

T

T

A

Q

D

G

F

T

F

S

I

I

S

G

T

T

N

G

T

T

A

V

T

D

Y

S

T

L

P

E

G

I

Secondary structure

SS confidence

Disorder

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Disorder confidence

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190

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Sequence

W

S

G

D

V

S

V

Q

F

D

A

T

W

T

S

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 3f85 chain A Region: 85 - 190 Aligned: 86 Modelled: 101 Confidence: 43.4% Identity: 22% PDB header:cell adhesion Chain: A: PDB Molecule:homo trimeric fusion of cfa/i fimbrial subunits b; PDBTitle: structure of fusion complex of homo trimeric major pilin subunits cfab2 of cfa/i fimbirae from etec e. coli Phyre2 PDB 1qfh chain B Region: 68 - 192 Aligned: 118 Modelled: 125 Confidence: 38.3% Identity: 17% PDB header:actin binding protein Chain: B: PDB Molecule:protein (gelation factor); PDBTitle: dimerization of gelation factor from dictyostelium2 discoideum: crystal structure of rod domains 5 and 6 Phyre2 PDB 1ofs chain C Region: 51 - 190 Aligned: 116 Modelled: 130 Confidence: 30.3% Identity: 22% PDB header:lectin Chain: C: PDB Molecule:pea lectin alpha chain; PDBTitle: pea lectin-sucrose complex Phyre2 PDB 3f84 chain A Region: 86 - 190 Aligned: 86 Modelled: 105 Confidence: 22.9% Identity: 23% PDB header:cell adhesion Chain: A: PDB Molecule:cfa/i fimbrial subunit b; PDBTitle: structure of fusion complex of major pilin cfab and major pilin cfab2 of cfa/i pilus from etec e. coli Phyre2 PDB 3f83 chain A Region: 35 - 190 Aligned: 132 Modelled: 143 Confidence: 20.9% Identity: 23% PDB header:cell adhesion Chain: A: PDB Molecule:fusion of the minor pilin cfae and major pilin cfab; PDBTitle: structure of fusion complex of the minor pilin cfae and major pilin2 cfab of cfa/i pili from etec e. coli Phyre2 PDB 1cwv chain A domain 1 Region: 84 - 191 Aligned: 92 Modelled: 108 Confidence: 18.6% Identity: 24% Fold: Immunoglobulin-like beta-sandwich Superfamily: Invasin/intimin cell-adhesion fragments Family: Invasin/intimin cell-adhesion fragments Phyre2 PDB 2qqp chain G Region: 49 - 127 Aligned: 78 Modelled: 79 Confidence: 12.1% Identity: 28% PDB header:virus Chain: G: PDB Molecule:large capsid protein; PDBTitle: crystal structure of authentic providence virus Phyre2 PDB 1tg7 chain A domain 1 Region: 87 - 119 Aligned: 33 Modelled: 33 Confidence: 10.6% Identity: 24% Fold: Beta-galactosidase LacA, domain 3 Superfamily: Beta-galactosidase LacA, domain 3 Family: Beta-galactosidase LacA, domain 3 Phyre2 PDB 1g7y chain A Region: 51 - 190 Aligned: 120 Modelled: 140 Confidence: 8.2% Identity: 18% Fold: Concanavalin A-like lectins/glucanases Superfamily: Concanavalin A-like lectins/glucanases Family: Legume lectins Phyre2 PDB 2c5s chain A Region: 111 - 141 Aligned: 26 Modelled: 31 Confidence: 7.7% Identity: 31% PDB header:rna-binding protein Chain: A: PDB Molecule:probable thiamine biosynthesis protein thii; PDBTitle: crystal structure of bacillus anthracis thii, a trna-2 modifying enzyme containing the predicted rna-binding3 thump domain Phyre2 PDB 1q14 chain A Region: 43 - 78 Aligned: 36 Modelled: 36 Confidence: 6.9% Identity: 25% PDB header:hydrolase Chain: A: PDB Molecule:hst2 protein; PDBTitle: structure and autoregulation of the yeast hst2 homolog of sir2 Phyre2 PDB 2jsh chain A Region: 68 - 76 Aligned: 9 Modelled: 9 Confidence: 6.3% Identity: 44% PDB header:hormone Chain: A: PDB Molecule:appetite-regulating hormone, obestatin; PDBTitle: obestatin nmr structure in sds/dpc micellar solution Phyre2 1 c3f85A_ 2 c1qfhB_ 3 c1ofsC_ 4 c3f84A_ 5 c3f83A_ 6 d1cwva1 7 c2qqpG_ 8 d1tg7a1 9 d1g7ya_ 10 c2c5sA_ 11 c1q14A_ 12 c2jshA_

Detailed template information

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

1 c3f85A_ 43.4 22 PDB header:cell adhesion Chain: A: PDB Molecule:homo trimeric fusion of cfa/i fimbrial subunits b; PDBTitle: structure of fusion complex of homo trimeric major pilin subunits cfab2 of cfa/i fimbirae from etec e. coli 2 c1qfhB_ 38.3 17 PDB header:actin binding protein Chain: B: PDB Molecule:protein (gelation factor); PDBTitle: dimerization of gelation factor from dictyostelium2 discoideum: crystal structure of rod domains 5 and 6 3 c1ofsC_ 30.3 22 PDB header:lectin Chain: C: PDB Molecule:pea lectin alpha chain; PDBTitle: pea lectin-sucrose complex 4 c3f84A_ 22.9 23 PDB header:cell adhesion Chain: A: PDB Molecule:cfa/i fimbrial subunit b; PDBTitle: structure of fusion complex of major pilin cfab and major pilin cfab2 of cfa/i pilus from etec e. coli 5 c3f83A_ 20.9 23 PDB header:cell adhesion Chain: A: PDB Molecule:fusion of the minor pilin cfae and major pilin cfab; PDBTitle: structure of fusion complex of the minor pilin cfae and major pilin2 cfab of cfa/i pili from etec e. coli 6 d1cwva1 18.6 24 Fold:Immunoglobulin-like beta-sandwich Superfamily:Invasin/intimin cell-adhesion fragments Family:Invasin/intimin cell-adhesion fragments 7 c2qqpG_ 12.1 28 PDB header:virus Chain: G: PDB Molecule:large capsid protein; PDBTitle: crystal structure of authentic providence virus 8 d1tg7a1 10.6 24 Fold:Beta-galactosidase LacA, domain 3 Superfamily:Beta-galactosidase LacA, domain 3 Family:Beta-galactosidase LacA, domain 3 9 d1g7ya_ 8.2 18 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Legume lectins 10 c2c5sA_ 7.7 31 PDB header:rna-binding protein Chain: A: PDB Molecule:probable thiamine biosynthesis protein thii; PDBTitle: crystal structure of bacillus anthracis thii, a trna-2 modifying enzyme containing the predicted rna-binding3 thump domain 11 c1q14A_ 6.9 25 PDB header:hydrolase Chain: A: PDB Molecule:hst2 protein; PDBTitle: structure and autoregulation of the yeast hst2 homolog of sir2 12 c2jshA_ 6.3 44 PDB header:hormone Chain: A: PDB Molecule:appetite-regulating hormone, obestatin; PDBTitle: obestatin nmr structure in sds/dpc micellar solution

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