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

F

F

K

K

N

L

T

T

A

A

I

C

A

A

L

S

V

A

A

F

S

A

M

A

T

D

S

T

D

T

E

L

T

I

I

G

E

Y

T

P

G

A

C

T

P

V

V

T

G

G

G

I

V

D

Y

G

K

H

H

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

N

S

A

L

N

P

T

G

K

S

N

K

L

V

Q

L

G

R

K

N

S

T

L

N

I

T

C

T

A

P

T

L

I

A

V

T

S

K

D

N

R

Q

S

T

I

V

A

L

N

D

T

S

Y

I

E

K

A

Y

D

T

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

L

V

D

M

K

G

T

K

N

A

F

G

L

G

S

A

P

N

G

Q

K

I

G

A

A

S

I

G

I

D

R

S

N

G

G

I

H

A

A

D

D

T

G

E

I

P

V

D

L

I

Q

T

D

H

W

S

A

A

T

P

Secondary structure

SS confidence

Disorder

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?

Disorder confidence

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190

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200

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210

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220

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230

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240

Sequence

T

W

K

A

S

S

N

G

A

F

C

S

L

T

S

C

S

A

I

E

R

G

Y

S

V

A

K

T

G

E

L

T

P

V

A

I

T

A

V

T

F

P

L

L

I

D

A

A

V

N

D

N

T

I

L

G

S

D

E

T

Secondary structure

SS confidence

Disorder

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Disorder confidence

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250

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Sequence

I

K

L

D

G

N

V

T

I

S

V

Q

Y

L

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 3jwn chain K Region: 29 - 141 Aligned: 98 Modelled: 113 Confidence: 97.4% Identity: 17% 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: 29 - 141 Aligned: 98 Modelled: 113 Confidence: 97.3% Identity: 17% 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: 29 - 141 Aligned: 98 Modelled: 113 Confidence: 97.3% Identity: 17% PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 2jty chain A Region: 24 - 141 Aligned: 105 Modelled: 118 Confidence: 97.2% Identity: 14% 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 F Region: 29 - 104 Aligned: 71 Modelled: 76 Confidence: 97.1% Identity: 18% PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 2w07 chain B Region: 39 - 171 Aligned: 119 Modelled: 125 Confidence: 96.1% Identity: 15% 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 2uy6 chain B domain 1 Region: 32 - 91 Aligned: 54 Modelled: 54 Confidence: 95.0% Identity: 17% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2jmr chain A Region: 29 - 141 Aligned: 98 Modelled: 113 Confidence: 94.5% Identity: 15% PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf Phyre2 PDB 1n12 chain A Region: 42 - 99 Aligned: 48 Modelled: 58 Confidence: 94.0% Identity: 29% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2j2z chain B domain 1 Region: 33 - 90 Aligned: 52 Modelled: 52 Confidence: 94.0% Identity: 19% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3bfw chain A Region: 42 - 98 Aligned: 51 Modelled: 57 Confidence: 92.9% Identity: 24% 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 2wmp chain B Region: 42 - 134 Aligned: 64 Modelled: 75 Confidence: 92.5% Identity: 27% PDB header:chaperone Chain: B: PDB Molecule:papg protein; PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin Phyre2 PDB 1ze3 chain H domain 1 Region: 42 - 142 Aligned: 74 Modelled: 85 Confidence: 91.7% Identity: 16% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1klf chain P Region: 38 - 104 Aligned: 50 Modelled: 51 Confidence: 89.7% Identity: 14% PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose Phyre2 PDB 1pdk chain B Region: 39 - 90 Aligned: 47 Modelled: 52 Confidence: 85.7% Identity: 4% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2jna chain A domain 1 Region: 3 - 30 Aligned: 26 Modelled: 28 Confidence: 13.3% Identity: 35% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 3qbt chain H Region: 45 - 104 Aligned: 45 Modelled: 46 Confidence: 8.6% Identity: 9% PDB header:protein transport/hydrolase Chain: H: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1; PDBTitle: crystal structure of ocrl1 540-678 in complex with rab8a:gppnhp Phyre2 PDB 2kr7 chain A Region: 212 - 234 Aligned: 23 Modelled: 23 Confidence: 8.2% Identity: 13% PDB header:isomerase Chain: A: PDB Molecule:fkbp-type peptidyl-prolyl cis-trans isomerase slyd; PDBTitle: solution structure of helicobacter pylori slyd Phyre2 PDB 2kfw chain A Region: 211 - 225 Aligned: 15 Modelled: 15 Confidence: 7.2% Identity: 13% PDB header:isomerase Chain: A: PDB Molecule:fkbp-type peptidyl-prolyl cis-trans isomerase PDBTitle: solution structure of full-length slyd from e.coli Phyre2 PDB 3klq chain B Region: 41 - 60 Aligned: 20 Modelled: 20 Confidence: 7.0% Identity: 10% PDB header:cell adhesion Chain: B: PDB Molecule:putative pilus anchoring protein; PDBTitle: crystal structure of the minor pilin fctb from streptococcus pyogenes2 90/306s Phyre2 1 c3jwnK_ 2 c3jwnL_ 3 c3jwnE_ 4 c2jtyA_ 5 c3jwnF_ 6 c2w07B_ 7 d2uy6b1 8 c2jmrA_ 9 d1n12a_ 10 d2j2zb1 11 c3bfwA_ 12 c2wmpB_ 13 d1ze3h1 14 c1klfP_ 15 d1pdkb_ 16 d2jnaa1 17 c3qbtH_ 18 c2kr7A_ 19 c2kfwA_ 20 c3klqB_ 21

Detailed template information

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

1 c3jwnK_ 97.4 17 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 2 c3jwnL_ 97.3 17 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 3 c3jwnE_ 97.3 17 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 4 c2jtyA_ 97.2 14 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 5 c3jwnF_ 97.1 18 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 6 c2w07B_ 96.1 15 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 7 d2uy6b1 95.0 17 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 8 c2jmrA_ 94.5 15 PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf 9 d1n12a_ 94.0 29 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 10 d2j2zb1 94.0 19 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 11 c3bfwA_ 92.9 24 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 c2wmpB_ 92.5 27 PDB header:chaperone Chain: B: PDB Molecule:papg protein; PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin 13 d1ze3h1 91.7 16 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 14 c1klfP_ 89.7 14 PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose 15 d1pdkb_ 85.7 4 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 16 d2jnaa1 13.3 35 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 17 c3qbtH_ 8.6 9 PDB header:protein transport/hydrolase Chain: H: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1; PDBTitle: crystal structure of ocrl1 540-678 in complex with rab8a:gppnhp 18 c2kr7A_ 8.2 13 PDB header:isomerase Chain: A: PDB Molecule:fkbp-type peptidyl-prolyl cis-trans isomerase slyd; PDBTitle: solution structure of helicobacter pylori slyd 19 c2kfwA_ 7.2 13 PDB header:isomerase Chain: A: PDB Molecule:fkbp-type peptidyl-prolyl cis-trans isomerase PDBTitle: solution structure of full-length slyd from e.coli 20 c3klqB_ 7.0 10 PDB header:cell adhesion Chain: B: PDB Molecule:putative pilus anchoring protein; PDBTitle: crystal structure of the minor pilin fctb from streptococcus pyogenes2 90/306s 21 c2xzzA_ not modelled 6.4 16 PDB header:transferase Chain: A: PDB Molecule:protein-glutamine gamma-glutamyltransferase k; PDBTitle: crystal structure of the human transglutaminase 1 beta-barrel domain

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