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

T

T

T

G

L

R

P

R

L

N

V

R

Q

R

K

D

T

G

Y

L

P

H

S

S

P

F

S

L

Q

F

R

P

A

I

L

Y

S

D

G

Y

L

P

L

V

P

E

D

K

N

E

T

D

K

I

H

T

P

R

I

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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80

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.

Sequence

V

P

Q

K

L

E

R

T

P

S

D

T

S

R

S

R

G

C

H

C

F

Y

A

G

W

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 2knq chain A Region: 25 - 44 Aligned: 20 Modelled: 20 Confidence: 79.5% Identity: 40% PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein h; PDBTitle: solution structure of e.coli gsph Phyre2 PDB 1qb3 chain B Region: 29 - 77 Aligned: 45 Modelled: 49 Confidence: 20.8% Identity: 20% PDB header:cell cycle Chain: B: PDB Molecule:cyclin-dependent kinases regulatory subunit; PDBTitle: crystal structure of the cell cycle regulatory protein cks1 Phyre2 PDB 2vzs chain A domain 2 Region: 35 - 49 Aligned: 15 Modelled: 15 Confidence: 17.3% Identity: 20% Fold: Immunoglobulin-like beta-sandwich Superfamily: beta-Galactosidase/glucuronidase domain Family: beta-Galactosidase/glucuronidase domain Phyre2 PDB 1drs chain A Region: 70 - 81 Aligned: 12 Modelled: 12 Confidence: 16.2% Identity: 50% Fold: Snake toxin-like Superfamily: Snake toxin-like Family: Dendroaspin Phyre2 PDB 1qb3 chain A Region: 29 - 77 Aligned: 45 Modelled: 49 Confidence: 15.0% Identity: 20% Fold: Cell cycle regulatory proteins Superfamily: Cell cycle regulatory proteins Family: Cell cycle regulatory proteins Phyre2 PDB 3pfn chain B Region: 25 - 53 Aligned: 29 Modelled: 29 Confidence: 11.9% Identity: 24% PDB header:transferase Chain: B: PDB Molecule:nad kinase; PDBTitle: crystal structure of human nad kinase Phyre2 PDB 1nm8 chain A domain 2 Region: 52 - 83 Aligned: 32 Modelled: 32 Confidence: 7.3% Identity: 9% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 2h4t chain B Region: 53 - 83 Aligned: 31 Modelled: 31 Confidence: 6.6% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:carnitine o-palmitoyltransferase ii, PDBTitle: crystal structure of rat carnitine palmitoyltransferase ii Phyre2 PDB 3afo chain B Region: 25 - 50 Aligned: 26 Modelled: 26 Confidence: 6.6% Identity: 31% PDB header:transferase Chain: B: PDB Molecule:nadh kinase pos5; PDBTitle: crystal structure of yeast nadh kinase complexed with nadh Phyre2 PDB 1u1z chain A Region: 20 - 29 Aligned: 10 Modelled: 10 Confidence: 6.3% Identity: 70% Fold: Thioesterase/thiol ester dehydrase-isomerase Superfamily: Thioesterase/thiol ester dehydrase-isomerase Family: FabZ-like Phyre2 PDB 3da7 chain G Region: 35 - 52 Aligned: 18 Modelled: 18 Confidence: 5.7% Identity: 39% PDB header:protein binding Chain: G: PDB Molecule:barnase circular permutant; PDBTitle: a conformationally strained, circular permutant of barnase Phyre2 PDB 3bjr chain A Region: 6 - 40 Aligned: 28 Modelled: 35 Confidence: 5.7% Identity: 36% PDB header:hydrolase Chain: A: PDB Molecule:putative carboxylesterase; PDBTitle: crystal structure of a putative carboxylesterase (lp_1002) from2 lactobacillus plantarum wcfs1 at 2.09 a resolution Phyre2 PDB 1t1u chain A domain 2 Region: 52 - 83 Aligned: 32 Modelled: 32 Confidence: 5.5% Identity: 9% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 2glv chain A Region: 20 - 29 Aligned: 10 Modelled: 10 Confidence: 5.2% Identity: 50% PDB header:lyase Chain: A: PDB Molecule:(3r)-hydroxymyristoyl-acyl carrier protein PDBTitle: crystal structure of (3r)-hydroxyacyl-acyl carrier protein2 dehydratase(fabz) mutant(y100a) from helicobacter pylori Phyre2 1 c2knqA_ 2 c1qb3B_ 3 d2vzsa2 4 d1drsa_ 5 d1qb3a_ 6 c3pfnB_ 7 d1nm8a2 8 c2h4tB_ 9 c3afoB_ 10 d1u1za_ 11 c3da7G_ 12 c3bjrA_ 13 d1t1ua2 14 c2glvA_

Detailed template information

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

1 c2knqA_ 79.5 40 PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein h; PDBTitle: solution structure of e.coli gsph 2 c1qb3B_ 20.8 20 PDB header:cell cycle Chain: B: PDB Molecule:cyclin-dependent kinases regulatory subunit; PDBTitle: crystal structure of the cell cycle regulatory protein cks1 3 d2vzsa2 17.3 20 Fold:Immunoglobulin-like beta-sandwich Superfamily:beta-Galactosidase/glucuronidase domain Family:beta-Galactosidase/glucuronidase domain 4 d1drsa_ 16.2 50 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Dendroaspin 5 d1qb3a_ 15.0 20 Fold:Cell cycle regulatory proteins Superfamily:Cell cycle regulatory proteins Family:Cell cycle regulatory proteins 6 c3pfnB_ 11.9 24 PDB header:transferase Chain: B: PDB Molecule:nad kinase; PDBTitle: crystal structure of human nad kinase 7 d1nm8a2 7.3 9 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 8 c2h4tB_ 6.6 13 PDB header:transferase Chain: B: PDB Molecule:carnitine o-palmitoyltransferase ii, PDBTitle: crystal structure of rat carnitine palmitoyltransferase ii 9 c3afoB_ 6.6 31 PDB header:transferase Chain: B: PDB Molecule:nadh kinase pos5; PDBTitle: crystal structure of yeast nadh kinase complexed with nadh 10 d1u1za_ 6.3 70 Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:FabZ-like 11 c3da7G_ 5.7 39 PDB header:protein binding Chain: G: PDB Molecule:barnase circular permutant; PDBTitle: a conformationally strained, circular permutant of barnase 12 c3bjrA_ 5.7 36 PDB header:hydrolase Chain: A: PDB Molecule:putative carboxylesterase; PDBTitle: crystal structure of a putative carboxylesterase (lp_1002) from2 lactobacillus plantarum wcfs1 at 2.09 a resolution 13 d1t1ua2 5.5 9 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 14 c2glvA_ 5.2 50 PDB header:lyase Chain: A: PDB Molecule:(3r)-hydroxymyristoyl-acyl carrier protein PDBTitle: crystal structure of (3r)-hydroxyacyl-acyl carrier protein2 dehydratase(fabz) mutant(y100a) from helicobacter pylori

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