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

H

P

T

Q

R

K

L

M

K

R

I

I

L

F

L

S

L

L

F

C

I

A

C

P

A

I

A

G

Q

D

I

D

L

V

A

N

V

K

N

S

T

C

K

S

G

I

S

N

Q

G

N

I

D

L

G

V

V

G

V

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

G

Y

F

S

G

N

V

T

P

E

S

Y

Q

P

G

G

K

E

F

T

I

T

V

S

D

C

A

L

Q

G

T

G

D

V

L

N

Q

L

H

I

D

F

R

A

L

S

G

V

M

A

A

G

S

R

Q

I

F

A

N

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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180

Sequence

I

S

S

G

A

S

N

V

G

V

V

I

F

S

T

Q

D

S

A

N

T

F

N

V

L

N

A

S

G

G

S

R

S

V

Y

P

V

M

S

D

D

M

N

G

S

S

W

K

F

S

T

R

M

Q

K

I

D

P

A

L

Secondary structure

SS confidence

Disorder

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Disorder confidence

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190

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Sequence

S

V

T

S

G

Q

L

M

S

H

V

L

V

D

I

Y

Y

E

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 3jwn chain K Region: 28 - 198 Aligned: 153 Modelled: 171 Confidence: 99.9% Identity: 16% 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 - 198 Aligned: 153 Modelled: 171 Confidence: 99.9% Identity: 16% 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 - 198 Aligned: 153 Modelled: 171 Confidence: 99.9% Identity: 16% PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain F Region: 28 - 198 Aligned: 153 Modelled: 164 Confidence: 99.9% Identity: 16% PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 2jty chain A Region: 23 - 198 Aligned: 158 Modelled: 172 Confidence: 99.9% Identity: 18% 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 2jmr chain A Region: 28 - 198 Aligned: 153 Modelled: 171 Confidence: 99.9% Identity: 17% PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf Phyre2 PDB 2uy6 chain B domain 1 Region: 31 - 198 Aligned: 148 Modelled: 168 Confidence: 99.8% Identity: 11% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2j2z chain B domain 1 Region: 31 - 198 Aligned: 149 Modelled: 163 Confidence: 99.8% Identity: 15% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1pdk chain B Region: 38 - 198 Aligned: 145 Modelled: 161 Confidence: 99.8% Identity: 14% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3bwu chain F Region: 40 - 198 Aligned: 128 Modelled: 142 Confidence: 99.7% Identity: 16% 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 3bfw chain A Region: 40 - 197 Aligned: 131 Modelled: 148 Confidence: 99.7% Identity: 13% 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 1ze3 chain H domain 1 Region: 41 - 198 Aligned: 121 Modelled: 143 Confidence: 99.6% Identity: 21% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1klf chain P Region: 31 - 198 Aligned: 132 Modelled: 153 Confidence: 99.5% Identity: 21% PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose Phyre2 PDB 2w07 chain B Region: 37 - 197 Aligned: 120 Modelled: 135 Confidence: 99.5% Identity: 13% 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 1n12 chain A Region: 41 - 197 Aligned: 136 Modelled: 157 Confidence: 99.0% Identity: 14% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1y0u chain A Region: 1 - 12 Aligned: 12 Modelled: 10 Confidence: 26.5% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: ArsR-like transcriptional regulators Phyre2 PDB 1w3g chain A Region: 147 - 198 Aligned: 52 Modelled: 52 Confidence: 14.5% Identity: 19% PDB header:toxin/lectin Chain: A: PDB Molecule:hemolytic lectin from laetiporus sulphureus; PDBTitle: hemolytic lectin from the mushroom laetiporus sulphureus2 complexed with two n-acetyllactosamine molecules. Phyre2 PDB 3nqn chain B Region: 163 - 186 Aligned: 24 Modelled: 24 Confidence: 10.7% Identity: 4% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function. (dr_2006) from2 deinococcus radiodurans at 1.88 a resolution Phyre2 PDB 3rpj chain A Region: 1 - 12 Aligned: 12 Modelled: 12 Confidence: 7.2% Identity: 58% PDB header:transcription regulator Chain: A: PDB Molecule:curlin genes transcriptional regulator; PDBTitle: structure of a curlin genes transcriptional regulator protein from2 proteus mirabilis hi4320. Phyre2 PDB 3c7b chain A domain 3 Region: 76 - 89 Aligned: 14 Modelled: 14 Confidence: 6.5% Identity: 21% Fold: Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily: Nitrite and sulphite reductase 4Fe-4S domain-like Family: Nitrite and sulphite reductase 4Fe-4S domain-like Phyre2 1 c3jwnK_ 2 c3jwnL_ 3 c3jwnE_ 4 c3jwnF_ 5 c2jtyA_ 6 c2jmrA_ 7 d2uy6b1 8 d2j2zb1 9 d1pdkb_ 10 c3bwuF_ 11 c3bfwA_ 12 d1ze3h1 13 c1klfP_ 14 c2w07B_ 15 d1n12a_ 16 d1y0ua_ 17 c1w3gA_ 18 c3nqnB_ 19 c3rpjA_ 20 d3c7ba3 21 22 23 24 25 26 27

Detailed template information

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

1 c3jwnK_ 99.9 16 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 2 c3jwnL_ 99.9 16 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 3 c3jwnE_ 99.9 16 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 4 c3jwnF_ 99.9 16 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 5 c2jtyA_ 99.9 18 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 6 c2jmrA_ 99.9 17 PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf 7 d2uy6b1 99.8 11 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 8 d2j2zb1 99.8 15 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 9 d1pdkb_ 99.8 14 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 10 c3bwuF_ 99.7 16 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) 11 c3bfwA_ 99.7 13 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) 12 d1ze3h1 99.6 21 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 13 c1klfP_ 99.5 21 PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose 14 c2w07B_ 99.5 13 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 15 d1n12a_ 99.0 14 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 16 d1y0ua_ 26.5 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 17 c1w3gA_ 14.5 19 PDB header:toxin/lectin Chain: A: PDB Molecule:hemolytic lectin from laetiporus sulphureus; PDBTitle: hemolytic lectin from the mushroom laetiporus sulphureus2 complexed with two n-acetyllactosamine molecules. 18 c3nqnB_ 10.7 4 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function. (dr_2006) from2 deinococcus radiodurans at 1.88 a resolution 19 c3rpjA_ 7.2 58 PDB header:transcription regulator Chain: A: PDB Molecule:curlin genes transcriptional regulator; PDBTitle: structure of a curlin genes transcriptional regulator protein from2 proteus mirabilis hi4320. 20 d3c7ba3 6.5 21 Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-like 21 c1bctA_ not modelled 6.4 21 PDB header:photoreceptor Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: three-dimensional structure of proteolytic fragment 163-2312 of bacterioopsin determined from nuclear magnetic3 resonance data in solution 22 d2v4ja3 not modelled 6.2 14 Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-like 23 d3c7bb3 not modelled 6.1 16 Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-like 24 d2v4jb3 not modelled 5.8 8 Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-like 25 d1aopa4 not modelled 5.8 12 Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-like 26 d1z1za1 not modelled 5.6 25 Fold:Phage tail protein-like Superfamily:Phage tail protein-like Family:Lambda phage gpU-like 27 d2akja4 not modelled 5.5 12 Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-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