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

Y

E

A

L

L

V

V

F

L

I

V

A

I

G

L

V

G

L

I

M

L

Q

Q

G

K

G

A

D

M

G

A

S

F

G

A

G

A

S

A

T

L

F

G

S

S

G

S

G

N

F

M

T

R

M

T

A

L

L

A

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

Sequence

T

L

F

F

I

I

S

L

V

L

G

N

I

N

S

N

K

T

N

K

G

S

E

W

E

N

L

S

A

P

A

K

T

E

Q

T

Q

P

A

A

P

A

K

P

T

S

D

I

P

N

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 2aki chain A Region: 1 - 77 Aligned: 77 Modelled: 77 Confidence: 100.0% Identity: 100% PDB header:protein transport Chain: A: PDB Molecule:protein-export membrane protein secg; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli Phyre2 PDB 3din chain E Region: 9 - 73 Aligned: 65 Modelled: 65 Confidence: 99.9% Identity: 26% PDB header:membrane protein, protein transport Chain: E: PDB Molecule:preprotein translocase subunit secg; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 3dl8 chain F Region: 8 - 73 Aligned: 65 Modelled: 66 Confidence: 99.9% Identity: 38% PDB header:protein transport Chain: F: PDB Molecule:protein-export membrane protein secg; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 2axt chain I domain 1 Region: 54 - 82 Aligned: 29 Modelled: 29 Confidence: 56.2% Identity: 17% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein I, PsbI Family: PsbI-like Phyre2 PDB 2y69 chain W Region: 42 - 78 Aligned: 37 Modelled: 37 Confidence: 21.0% Identity: 19% PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1m56 chain D Region: 46 - 75 Aligned: 29 Modelled: 30 Confidence: 18.6% Identity: 14% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1zll chain E Region: 4 - 22 Aligned: 19 Modelled: 19 Confidence: 16.1% Identity: 11% PDB header:membrane protein/signaling protein Chain: E: PDB Molecule:cardiac phospholamban; PDBTitle: nmr structure of unphosphorylated human phospholamban2 pentamer Phyre2 PDB 1v54 chain J Region: 42 - 79 Aligned: 38 Modelled: 38 Confidence: 10.4% Identity: 18% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIa Family: Mitochondrial cytochrome c oxidase subunit VIIa Phyre2 PDB 1z65 chain A Region: 56 - 79 Aligned: 24 Modelled: 24 Confidence: 10.3% Identity: 17% PDB header:unknown function Chain: A: PDB Molecule:prion-like protein doppel; PDBTitle: mouse doppel 1-30 peptide Phyre2 PDB 1yew chain I Region: 45 - 105 Aligned: 61 Modelled: 61 Confidence: 10.2% Identity: 10% PDB header:oxidoreductase, membrane protein Chain: I: PDB Molecule:particulate methane monooxygenase, b subunit; PDBTitle: crystal structure of particulate methane monooxygenase Phyre2 PDB 3rgb chain A Region: 45 - 105 Aligned: 61 Modelled: 61 Confidence: 10.2% Identity: 10% PDB header:oxidoreductase Chain: A: PDB Molecule:methane monooxygenase subunit b2; PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath) Phyre2 PDB 1a62 chain A domain 1 Region: 16 - 29 Aligned: 14 Modelled: 14 Confidence: 9.3% Identity: 21% Fold: LEM/SAP HeH motif Superfamily: Rho N-terminal domain-like Family: Rho termination factor, N-terminal domain Phyre2 PDB 2k21 chain A Region: 30 - 83 Aligned: 54 Modelled: 54 Confidence: 6.2% Identity: 19% PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c Phyre2 1 c2akiA_ 2 c3dinE_ 3 c3dl8F_ 4 d2axti1 5 c2y69W_ 6 d1m56d_ 7 c1zllE_ 8 d1v54j_ 9 c1z65A_ 10 c1yewI_ 11 c3rgbA_ 12 d1a62a1 13 c2k21A_

Detailed template information

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

1 c2akiA_ 100.0 100 PDB header:protein transport Chain: A: PDB Molecule:protein-export membrane protein secg; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli 2 c3dinE_ 99.9 26 PDB header:membrane protein, protein transport Chain: E: PDB Molecule:preprotein translocase subunit secg; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase 3 c3dl8F_ 99.9 38 PDB header:protein transport Chain: F: PDB Molecule:protein-export membrane protein secg; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 4 d2axti1 56.2 17 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein I, PsbI Family:PsbI-like 5 c2y69W_ 21.0 19 PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 6 d1m56d_ 18.6 14 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 7 c1zllE_ 16.1 11 PDB header:membrane protein/signaling protein Chain: E: PDB Molecule:cardiac phospholamban; PDBTitle: nmr structure of unphosphorylated human phospholamban2 pentamer 8 d1v54j_ 10.4 18 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIa Family:Mitochondrial cytochrome c oxidase subunit VIIa 9 c1z65A_ 10.3 17 PDB header:unknown function Chain: A: PDB Molecule:prion-like protein doppel; PDBTitle: mouse doppel 1-30 peptide 10 c1yewI_ 10.2 10 PDB header:oxidoreductase, membrane protein Chain: I: PDB Molecule:particulate methane monooxygenase, b subunit; PDBTitle: crystal structure of particulate methane monooxygenase 11 c3rgbA_ 10.2 10 PDB header:oxidoreductase Chain: A: PDB Molecule:methane monooxygenase subunit b2; PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath) 12 d1a62a1 9.3 21 Fold:LEM/SAP HeH motif Superfamily:Rho N-terminal domain-like Family:Rho termination factor, N-terminal domain 13 c2k21A_ 6.2 19 PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c

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