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

N

K

Y

W

L

S

G

I

I

F

L

A

Y

G

L

A

S

P

A

F

S

S

E

T

A

T

L

A

I

N

G

R

I

S

P

P

T

C

S

M

A

M

V

N

G

Q

P

Q

Q

H

C

G

Q

L

T

Y

N

V

D

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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Sequence

T

R

H

L

F

S

S

P

V

K

G

V

T

T

E

V

V

V

A

G

S

D

S

K

R

R

I

V

L

N

R

Y

D

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 2jty chain A Region: 20 - 46 Aligned: 27 Modelled: 27 Confidence: 35.9% Identity: 15% 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 3jwn chain L Region: 26 - 43 Aligned: 18 Modelled: 18 Confidence: 30.3% Identity: 33% PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain F Region: 26 - 43 Aligned: 18 Modelled: 18 Confidence: 28.7% Identity: 33% PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain K Region: 26 - 43 Aligned: 18 Modelled: 18 Confidence: 27.1% Identity: 33% PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain E Region: 26 - 43 Aligned: 18 Modelled: 18 Confidence: 27.1% Identity: 33% 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: 26 - 43 Aligned: 18 Modelled: 18 Confidence: 22.3% Identity: 33% PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf Phyre2 PDB 2j2z chain B domain 1 Region: 29 - 43 Aligned: 15 Modelled: 15 Confidence: 15.4% Identity: 40% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3aq3 chain A Region: 44 - 67 Aligned: 24 Modelled: 23 Confidence: 11.9% Identity: 25% PDB header:toxin Chain: A: PDB Molecule:6b protein; PDBTitle: molecular insights into plant cell proliferation disturbance by2 agrobacterium protein 6b Phyre2 PDB 2eou chain A Region: 50 - 61 Aligned: 12 Modelled: 12 Confidence: 10.3% Identity: 25% PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 473; PDBTitle: solution structure of the c2h2 type zinc finger (region 370-2 400) of human zinc finger protein 473 Phyre2 PDB 2f09 chain A domain 1 Region: 24 - 41 Aligned: 18 Modelled: 18 Confidence: 8.4% Identity: 28% Fold: Streptavidin-like Superfamily: YdhA-like Family: YdhA-like Phyre2 PDB 2pa2 chain A domain 1 Region: 43 - 70 Aligned: 28 Modelled: 28 Confidence: 8.2% Identity: 18% Fold: alpha/beta-Hammerhead Superfamily: Ribosomal protein L16p/L10e Family: Ribosomal protein L10e Phyre2 PDB 2wkd chain A Region: 19 - 34 Aligned: 16 Modelled: 16 Confidence: 8.0% Identity: 31% PDB header:dna binding protein Chain: A: PDB Molecule:orf34p2; PDBTitle: crystal structure of a double ile-to-met mutant of protein2 orf34 from lactococcus phage p2 Phyre2 PDB 2ctd chain A domain 1 Region: 32 - 40 Aligned: 9 Modelled: 9 Confidence: 7.7% Identity: 56% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 2ob9 chain A Region: 60 - 89 Aligned: 30 Modelled: 30 Confidence: 7.4% Identity: 20% PDB header:chaperone Chain: A: PDB Molecule:tail assembly chaperone; PDBTitle: structure of bacteriophage hk97 tail assembly chaperone Phyre2 1 c2jtyA_ 2 c3jwnL_ 3 c3jwnF_ 4 c3jwnK_ 5 c3jwnE_ 6 c2jmrA_ 7 d2j2zb1 8 c3aq3A_ 9 c2eouA_ 10 d2f09a1 11 d2pa2a1 12 c2wkdA_ 13 d2ctda1 14 c2ob9A_

Detailed template information

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

1 c2jtyA_ 35.9 15 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 c3jwnL_ 30.3 33 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 3 c3jwnF_ 28.7 33 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 4 c3jwnK_ 27.1 33 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 5 c3jwnE_ 27.1 33 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 6 c2jmrA_ 22.3 33 PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf 7 d2j2zb1 15.4 40 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 8 c3aq3A_ 11.9 25 PDB header:toxin Chain: A: PDB Molecule:6b protein; PDBTitle: molecular insights into plant cell proliferation disturbance by2 agrobacterium protein 6b 9 c2eouA_ 10.3 25 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 473; PDBTitle: solution structure of the c2h2 type zinc finger (region 370-2 400) of human zinc finger protein 473 10 d2f09a1 8.4 28 Fold:Streptavidin-like Superfamily:YdhA-like Family:YdhA-like 11 d2pa2a1 8.2 18 Fold:alpha/beta-Hammerhead Superfamily:Ribosomal protein L16p/L10e Family:Ribosomal protein L10e 12 c2wkdA_ 8.0 31 PDB header:dna binding protein Chain: A: PDB Molecule:orf34p2; PDBTitle: crystal structure of a double ile-to-met mutant of protein2 orf34 from lactococcus phage p2 13 d2ctda1 7.7 56 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 14 c2ob9A_ 7.4 20 PDB header:chaperone Chain: A: PDB Molecule:tail assembly chaperone; PDBTitle: structure of bacteriophage hk97 tail assembly chaperone

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