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

K

P

L

S

S

A

I

A

A

A

L

I

L

F

S

A

Q

G

V

A

E

Q

T

T

Q

P

V

V

T

S

C

A

N

V

V

V

V

P

P

S

Q

E

H

P

P

F

D

L

N

H

M

G

T

G

S

D

K

S

D

Secondary structure

SS confidence

Disorder

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?

Disorder confidence

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70

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Sequence

A

L

G

V

P

Y

Y

N

Q

H

A

M

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 1c4e chain A Region: 58 - 67 Aligned: 10 Modelled: 10 Confidence: 36.9% Identity: 60% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Gurmarin-like Family: Gurmarin, a sweet taste-suppressing polypeptide Phyre2 PDB 1a0c chain A Region: 61 - 71 Aligned: 11 Modelled: 11 Confidence: 20.7% Identity: 27% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 1a0e chain A Region: 61 - 71 Aligned: 11 Modelled: 11 Confidence: 19.0% Identity: 27% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 1a0d chain A Region: 61 - 71 Aligned: 11 Modelled: 11 Confidence: 10.0% Identity: 27% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 2vsc chain D Region: 22 - 71 Aligned: 50 Modelled: 50 Confidence: 9.4% Identity: 10% PDB header:cell adhesion Chain: D: PDB Molecule:leukocyte surface antigen cd47; PDBTitle: structure of the immunoglobulin-superfamily ectodomain of2 human cd47 Phyre2 PDB 1an8 chain A domain 1 Region: 56 - 66 Aligned: 11 Modelled: 11 Confidence: 8.4% Identity: 36% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Superantigen toxins, N-terminal domain Phyre2 PDB 1ty0 chain A domain 1 Region: 56 - 66 Aligned: 11 Modelled: 11 Confidence: 7.4% Identity: 36% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Superantigen toxins, N-terminal domain Phyre2 PDB 2c2p chain A Region: 21 - 66 Aligned: 33 Modelled: 33 Confidence: 7.3% Identity: 27% PDB header:hydrolase Chain: A: PDB Molecule:g/u mismatch-specific dna glycosylase; PDBTitle: the crystal structure of mismatch specific uracil-dna2 glycosylase (mug) from deinococcus radiodurans Phyre2 PDB 2jna chain A domain 1 Region: 1 - 67 Aligned: 67 Modelled: 67 Confidence: 7.0% Identity: 21% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 1ujp chain A Region: 61 - 67 Aligned: 7 Modelled: 7 Confidence: 6.6% Identity: 43% Fold: TIM beta/alpha-barrel Superfamily: Ribulose-phoshate binding barrel Family: Tryptophan biosynthesis enzymes Phyre2 PDB 1l0n chain K Region: 64 - 68 Aligned: 5 Modelled: 5 Confidence: 5.9% Identity: 60% Fold: Single transmembrane helix Superfamily: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 2fyu chain K domain 1 Region: 64 - 68 Aligned: 5 Modelled: 5 Confidence: 5.8% Identity: 80% Fold: Single transmembrane helix Superfamily: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3r24 chain A Region: 32 - 58 Aligned: 22 Modelled: 27 Confidence: 5.8% Identity: 36% PDB header:transferase, viral protein Chain: A: PDB Molecule:2'-o-methyl transferase; PDBTitle: crystal structure of nsp10/nsp16 complex of sars coronavirus" if2 possible Phyre2 PDB 1eg3 chain A domain 3 Region: 64 - 70 Aligned: 7 Modelled: 7 Confidence: 5.7% Identity: 71% Fold: WW domain-like Superfamily: WW domain Family: WW domain Phyre2 1 d1c4ea_ 2 d1a0ca_ 3 d1a0ea_ 4 d1a0da_ 5 c2vscD_ 6 d1an8a1 7 d1ty0a1 8 c2c2pA_ 9 d2jnaa1 10 d1ujpa_ 11 d1l0nk_ 12 d2fyuk1 13 c3r24A_ 14 d1eg3a3

Detailed template information

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

1 d1c4ea_ 36.9 60 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Gurmarin-like Family:Gurmarin, a sweet taste-suppressing polypeptide 2 d1a0ca_ 20.7 27 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 3 d1a0ea_ 19.0 27 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 4 d1a0da_ 10.0 27 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 5 c2vscD_ 9.4 10 PDB header:cell adhesion Chain: D: PDB Molecule:leukocyte surface antigen cd47; PDBTitle: structure of the immunoglobulin-superfamily ectodomain of2 human cd47 6 d1an8a1 8.4 36 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Superantigen toxins, N-terminal domain 7 d1ty0a1 7.4 36 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Superantigen toxins, N-terminal domain 8 c2c2pA_ 7.3 27 PDB header:hydrolase Chain: A: PDB Molecule:g/u mismatch-specific dna glycosylase; PDBTitle: the crystal structure of mismatch specific uracil-dna2 glycosylase (mug) from deinococcus radiodurans 9 d2jnaa1 7.0 21 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 10 d1ujpa_ 6.6 43 Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:Tryptophan biosynthesis enzymes 11 d1l0nk_ 5.9 60 Fold:Single transmembrane helix Superfamily:Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 12 d2fyuk1 5.8 80 Fold:Single transmembrane helix Superfamily:Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 13 c3r24A_ 5.8 36 PDB header:transferase, viral protein Chain: A: PDB Molecule:2'-o-methyl transferase; PDBTitle: crystal structure of nsp10/nsp16 complex of sars coronavirus" if2 possible 14 d1eg3a3 5.7 71 Fold:WW domain-like Superfamily:WW domain Family:WW 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