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

P

Y

K

T

K

S

D

L

P

E

S

V

K

H

V

L

P

S

H

A

Q

D

I

Y

K

E

A

F

N

S

A

W

D

Q

Y

K

D

K

E

D

R

R

D

D

A

S

R

E

E

T

A

H

K

V

A

W

A

A

V

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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Sequence

K

H

E

Y

A

K

G

D

D

D

K

W

H

K

K

S

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 1sg7 chain A Region: 2 - 76 Aligned: 75 Modelled: 75 Confidence: 100.0% Identity: 100% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cation transport regulator chab; PDBTitle: nmr solution structure of the putative cation transport2 regulator chab Phyre2 PDB 1sg7 chain A domain 1 Region: 2 - 76 Aligned: 75 Modelled: 75 Confidence: 100.0% Identity: 100% Fold: ChaB-like Superfamily: ChaB-like Family: ChaB-like Phyre2 PDB 1k32 chain A domain 4 Region: 15 - 66 Aligned: 41 Modelled: 52 Confidence: 30.6% Identity: 22% Fold: ClpP/crotonase Superfamily: ClpP/crotonase Family: Tail specific protease, catalytic domain Phyre2 PDB 1fc6 chain A domain 4 Region: 22 - 66 Aligned: 34 Modelled: 45 Confidence: 28.1% Identity: 32% Fold: ClpP/crotonase Superfamily: ClpP/crotonase Family: Tail specific protease, catalytic domain Phyre2 PDB 2q9q chain C Region: 9 - 37 Aligned: 28 Modelled: 29 Confidence: 22.7% Identity: 11% PDB header:replication Chain: C: PDB Molecule:dna replication complex gins protein psf1; PDBTitle: the crystal structure of full length human gins complex Phyre2 PDB 1knc chain A Region: 11 - 59 Aligned: 39 Modelled: 49 Confidence: 18.5% Identity: 26% Fold: AhpD-like Superfamily: AhpD-like Family: AhpD Phyre2 PDB 1bpo chain A Region: 13 - 56 Aligned: 32 Modelled: 44 Confidence: 17.5% Identity: 31% PDB header:membrane protein Chain: A: PDB Molecule:protein (clathrin); PDBTitle: clathrin heavy-chain terminal domain and linker Phyre2 PDB 1bpo chain A domain 1 Region: 12 - 56 Aligned: 34 Modelled: 45 Confidence: 16.4% Identity: 26% Fold: alpha-alpha superhelix Superfamily: ARM repeat Family: Clathrin heavy-chain linker domain Phyre2 PDB 2e9x chain A domain 1 Region: 9 - 36 Aligned: 27 Modelled: 28 Confidence: 15.8% Identity: 11% Fold: GINS helical bundle-like Superfamily: GINS helical bundle-like Family: PSF1 N-terminal domain-like Phyre2 PDB 3mop chain M Region: 6 - 17 Aligned: 12 Modelled: 12 Confidence: 11.0% Identity: 33% PDB header:signaling protein, immune system Chain: M: PDB Molecule:interleukin-1 receptor-associated kinase-like 2; PDBTitle: the ternary death domain complex of myd88, irak4, and irak2 Phyre2 PDB 1o8t chain A Region: 21 - 35 Aligned: 15 Modelled: 15 Confidence: 8.8% Identity: 33% PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein c-ii; PDBTitle: global structure and dynamics of human apolipoprotein cii2 in complex with micelles: evidence for increased mobility3 of the helix involvved in the activation of lipoprotein4 lipase. Phyre2 PDB 1trl chain B Region: 44 - 60 Aligned: 17 Modelled: 17 Confidence: 8.2% Identity: 35% PDB header:hydrolase (metalloprotease) Chain: B: PDB Molecule:thermolysin fragment 255 - 316; PDBTitle: nmr solution structure of the c-terminal fragment 255-3162 of thermolysin: a dimer formed by subunits having the3 native structure Phyre2 PDB 2qfk chain A domain 1 Region: 11 - 31 Aligned: 21 Modelled: 21 Confidence: 6.4% Identity: 29% Fold: Globin-like Superfamily: Globin-like Family: Globins Phyre2 PDB 1fc9 chain A Region: 22 - 66 Aligned: 34 Modelled: 45 Confidence: 5.7% Identity: 32% PDB header:hydrolase Chain: A: PDB Molecule:photosystem ii d1 protease; PDBTitle: photosystem ii d1 c-terminal processing protease Phyre2 PDB 2ddz chain A domain 1 Region: 19 - 47 Aligned: 29 Modelled: 29 Confidence: 5.7% Identity: 21% Fold: Class II aaRS and biotin synthetases Superfamily: Class II aaRS and biotin synthetases Family: PH0223-like Phyre2 PDB 2kwu chain A Region: 7 - 17 Aligned: 11 Modelled: 11 Confidence: 5.5% Identity: 45% PDB header:protein binding/signaling protein Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: solution structure of ubm2 of murine polymerase iota in complex with2 ubiquitin Phyre2 PDB 1tns chain A Region: 6 - 17 Aligned: 12 Modelled: 12 Confidence: 5.3% Identity: 33% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 1qpm chain A Region: 5 - 17 Aligned: 13 Modelled: 13 Confidence: 5.2% Identity: 8% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 1 c1sg7A_ 2 d1sg7a1 3 d1k32a4 4 d1fc6a4 5 c2q9qC_ 6 d1knca_ 7 c1bpoA_ 8 d1bpoa1 9 d2e9xa1 10 c3mopM_ 11 c1o8tA_ 12 c1trlB_ 13 d2qfka1 14 c1fc9A_ 15 d2ddza1 16 c2kwuA_ 17 d1tnsa_ 18 d1qpma_

Detailed template information

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

1 c1sg7A_ 100.0 100 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cation transport regulator chab; PDBTitle: nmr solution structure of the putative cation transport2 regulator chab 2 d1sg7a1 100.0 100 Fold:ChaB-like Superfamily:ChaB-like Family:ChaB-like 3 d1k32a4 30.6 22 Fold:ClpP/crotonase Superfamily:ClpP/crotonase Family:Tail specific protease, catalytic domain 4 d1fc6a4 28.1 32 Fold:ClpP/crotonase Superfamily:ClpP/crotonase Family:Tail specific protease, catalytic domain 5 c2q9qC_ 22.7 11 PDB header:replication Chain: C: PDB Molecule:dna replication complex gins protein psf1; PDBTitle: the crystal structure of full length human gins complex 6 d1knca_ 18.5 26 Fold:AhpD-like Superfamily:AhpD-like Family:AhpD 7 c1bpoA_ 17.5 31 PDB header:membrane protein Chain: A: PDB Molecule:protein (clathrin); PDBTitle: clathrin heavy-chain terminal domain and linker 8 d1bpoa1 16.4 26 Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:Clathrin heavy-chain linker domain 9 d2e9xa1 15.8 11 Fold:GINS helical bundle-like Superfamily:GINS helical bundle-like Family:PSF1 N-terminal domain-like 10 c3mopM_ 11.0 33 PDB header:signaling protein, immune system Chain: M: PDB Molecule:interleukin-1 receptor-associated kinase-like 2; PDBTitle: the ternary death domain complex of myd88, irak4, and irak2 11 c1o8tA_ 8.8 33 PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein c-ii; PDBTitle: global structure and dynamics of human apolipoprotein cii2 in complex with micelles: evidence for increased mobility3 of the helix involvved in the activation of lipoprotein4 lipase. 12 c1trlB_ 8.2 35 PDB header:hydrolase (metalloprotease) Chain: B: PDB Molecule:thermolysin fragment 255 - 316; PDBTitle: nmr solution structure of the c-terminal fragment 255-3162 of thermolysin: a dimer formed by subunits having the3 native structure 13 d2qfka1 6.4 29 Fold:Globin-like Superfamily:Globin-like Family:Globins 14 c1fc9A_ 5.7 32 PDB header:hydrolase Chain: A: PDB Molecule:photosystem ii d1 protease; PDBTitle: photosystem ii d1 c-terminal processing protease 15 d2ddza1 5.7 21 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:PH0223-like 16 c2kwuA_ 5.5 45 PDB header:protein binding/signaling protein Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: solution structure of ubm2 of murine polymerase iota in complex with2 ubiquitin 17 d1tnsa_ 5.3 33 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 18 d1qpma_ 5.2 8 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-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