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

S

K

F

V

K

T

A

I

A

A

A

M

V

M

G

A

F

T

S

T

A

T

I

A

A

G

N

N

G

T

A

R

F

Y

G

T

I

E

D

S

V

C

S

I

V

P

D

D

H

K

L

E

V

D

M

G

D

I

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

A

E

K

L

K

N

N

G

T

T

T

P

K

N

F

Q

I

R

L

Q

D

C

V

F

D

T

Q

E

T

M

T

T

T

F

T

G

T

V

S

S

A

N

S

G

N

Y

Y

T

I

F

N

T

D

T

G

A

A

F

N

N

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

V

S

L

A

I

G

D

S

L

G

T

S

Y

K

S

G

M

G

I

D

Q

K

I

V

K

D

T

A

T

N

K

G

K

A

K

Q

T

L

N

F

K

A

W

L

V

G

A

A

D

A

P

D

L

G

N

F

E

A

N

T

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

T

F

Q

I

T

Y

L

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 2jty chain A Region: 23 - 186 Aligned: 157 Modelled: 164 Confidence: 99.9% Identity: 23% PDB header:structural protein Chain: A: PDB Molecule:type-1 fimbrial protein, a chain; PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus Phyre2 PDB 2j2z chain B domain 1 Region: 31 - 186 Aligned: 149 Modelled: 156 Confidence: 99.9% Identity: 20% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3jwn chain K Region: 28 - 186 Aligned: 153 Modelled: 159 Confidence: 99.9% Identity: 22% PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain L Region: 28 - 186 Aligned: 153 Modelled: 159 Confidence: 99.9% Identity: 22% PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain E Region: 28 - 186 Aligned: 153 Modelled: 159 Confidence: 99.9% Identity: 22% PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 2jmr chain A Region: 28 - 186 Aligned: 153 Modelled: 159 Confidence: 99.9% Identity: 22% PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf Phyre2 PDB 3jwn chain F Region: 28 - 186 Aligned: 153 Modelled: 159 Confidence: 99.9% Identity: 22% PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 2uy6 chain B domain 1 Region: 31 - 186 Aligned: 142 Modelled: 156 Confidence: 99.8% Identity: 24% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1pdk chain B Region: 38 - 186 Aligned: 141 Modelled: 149 Confidence: 99.8% Identity: 26% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3bfw chain A Region: 40 - 186 Aligned: 131 Modelled: 139 Confidence: 99.8% Identity: 18% PDB header:structural protein/structural protein Chain: A: PDB Molecule:protein fimg; PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf) Phyre2 PDB 3bwu chain F Region: 40 - 186 Aligned: 127 Modelled: 147 Confidence: 99.7% Identity: 24% PDB header:chaperone, structural, membrane protein Chain: F: PDB Molecule:protein fimf; PDBTitle: crystal structure of the ternary complex of fimd (n-terminal domain,2 fimdn) with fimc and the n-terminally truncated pilus subunit fimf3 (fimft) Phyre2 PDB 2w07 chain B Region: 37 - 186 Aligned: 119 Modelled: 133 Confidence: 99.7% Identity: 18% PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf Phyre2 PDB 1klf chain P Region: 31 - 186 Aligned: 132 Modelled: 156 Confidence: 99.7% Identity: 14% PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose Phyre2 PDB 1ze3 chain H domain 1 Region: 41 - 186 Aligned: 120 Modelled: 146 Confidence: 99.7% Identity: 16% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1n12 chain A Region: 41 - 186 Aligned: 135 Modelled: 146 Confidence: 99.4% Identity: 17% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2jna chain A domain 1 Region: 1 - 27 Aligned: 24 Modelled: 27 Confidence: 10.2% Identity: 29% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 1 c2jtyA_ 2 d2j2zb1 3 c3jwnK_ 4 c3jwnL_ 5 c3jwnE_ 6 c2jmrA_ 7 c3jwnF_ 8 d2uy6b1 9 d1pdkb_ 10 c3bfwA_ 11 c3bwuF_ 12 c2w07B_ 13 c1klfP_ 14 d1ze3h1 15 d1n12a_ 16 d2jnaa1

Detailed template information

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

1 c2jtyA_ 99.9 23 PDB header:structural protein Chain: A: PDB Molecule:type-1 fimbrial protein, a chain; PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus 2 d2j2zb1 99.9 20 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 3 c3jwnK_ 99.9 22 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 4 c3jwnL_ 99.9 22 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 5 c3jwnE_ 99.9 22 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 6 c2jmrA_ 99.9 22 PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf 7 c3jwnF_ 99.9 22 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 8 d2uy6b1 99.8 24 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 9 d1pdkb_ 99.8 26 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 10 c3bfwA_ 99.8 18 PDB header:structural protein/structural protein Chain: A: PDB Molecule:protein fimg; PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf) 11 c3bwuF_ 99.7 24 PDB header:chaperone, structural, membrane protein Chain: F: PDB Molecule:protein fimf; PDBTitle: crystal structure of the ternary complex of fimd (n-terminal domain,2 fimdn) with fimc and the n-terminally truncated pilus subunit fimf3 (fimft) 12 c2w07B_ 99.7 18 PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf 13 c1klfP_ 99.7 14 PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose 14 d1ze3h1 99.7 16 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 15 d1n12a_ 99.4 17 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 16 d2jnaa1 10.2 29 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like

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