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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Sequence

M

A

E

H

R

G

G

S

G

N

F

A

E

D

R

E

K

A

S

D

A

G

R

K

G

G

Q

H

S

G

G

N

F

K

N

D

P

Q

R

A

S

E

A

G

K

K

G

G

Q

Q

S

G

G

N

K

S

G

K

S

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 1uj8 chain A domain 1 Region: 32 - 42 Aligned: 11 Modelled: 11 Confidence: 18.9% Identity: 45% Fold: Another 3-helical bundle Superfamily: IscX-like Family: IscX-like Phyre2 PDB 3ch0 chain A Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 15.5% Identity: 30% PDB header:hydrolase Chain: A: PDB Molecule:glycerophosphodiester phosphodiesterase; PDBTitle: crystal structure of glycerophosphoryl diester phosphodiesterase2 (yp_677622.1) from cytophaga hutchinsonii atcc 33406 at 1.50 a3 resolution Phyre2 PDB 1o1z chain A Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 13.5% Identity: 30% Fold: TIM beta/alpha-barrel Superfamily: PLC-like phosphodiesterases Family: Glycerophosphoryl diester phosphodiesterase Phyre2 PDB 1zcc chain A domain 1 Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 10.5% Identity: 30% Fold: TIM beta/alpha-barrel Superfamily: PLC-like phosphodiesterases Family: Glycerophosphoryl diester phosphodiesterase Phyre2 PDB 2pz0 chain B Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 9.6% Identity: 35% PDB header:hydrolase Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis Phyre2 PDB 2otd chain C Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 9.3% Identity: 43% PDB header:hydrolase Chain: C: PDB Molecule:glycerophosphodiester phosphodiesterase; PDBTitle: the crystal structure of the glycerophosphodiester phosphodiesterase2 from shigella flexneri 2a Phyre2 PDB 3i10 chain A Region: 4 - 26 Aligned: 23 Modelled: 21 Confidence: 8.1% Identity: 26% PDB header:hydrolase Chain: A: PDB Molecule:putative glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (np_812074.1) from bacteroides thetaiotaomicron3 vpi-5482 at 1.35 a resolution Phyre2 PDB 1ydy chain A domain 1 Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 8.0% Identity: 35% Fold: TIM beta/alpha-barrel Superfamily: PLC-like phosphodiesterases Family: Glycerophosphoryl diester phosphodiesterase Phyre2 PDB 1ydy chain A Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 8.0% Identity: 35% PDB header:hydrolase Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of periplasmic glycerophosphodiester2 phosphodiesterase from escherichia coli Phyre2 PDB 3mz2 chain A Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 8.0% Identity: 26% PDB header:hydrolase Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of a glycerophosphoryl diester phosphodiesterase2 (bdi_3922) from parabacteroides distasonis atcc 8503 at 1.55 a3 resolution Phyre2 PDB 3mst chain A Region: 33 - 42 Aligned: 10 Modelled: 10 Confidence: 7.8% Identity: 50% PDB header:transport protein Chain: A: PDB Molecule:putative nitrate transport protein; PDBTitle: crystal structure of a putative nitrate transport protein (tvn0104)2 from thermoplasma volcanium at 1.35 a resolution Phyre2 PDB 1vd6 chain A domain 1 Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 7.5% Identity: 22% Fold: TIM beta/alpha-barrel Superfamily: PLC-like phosphodiesterases Family: Glycerophosphoryl diester phosphodiesterase Phyre2 PDB 2p76 chain H Region: 4 - 21 Aligned: 18 Modelled: 18 Confidence: 6.6% Identity: 44% PDB header:hydrolase Chain: H: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of a glycerophosphodiester phosphodiesterase from2 staphylococcus aureus Phyre2 PDB 1whg chain A Region: 6 - 20 Aligned: 15 Modelled: 15 Confidence: 6.3% Identity: 27% Fold: SH3-like barrel Superfamily: Cap-Gly domain Family: Cap-Gly domain Phyre2 PDB 1koh chain A domain 2 Region: 5 - 17 Aligned: 13 Modelled: 13 Confidence: 5.6% Identity: 38% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Non-canonical RBD domain Phyre2 1 d1uj8a1 2 c3ch0A_ 3 d1o1za_ 4 d1zcca1 5 c2pz0B_ 6 c2otdC_ 7 c3i10A_ 8 d1ydya1 9 c1ydyA_ 10 c3mz2A_ 11 c3mstA_ 12 d1vd6a1 13 c2p76H_ 14 d1whga_ 15 d1koha2

Detailed template information

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

1 d1uj8a1 18.9 45 Fold:Another 3-helical bundle Superfamily:IscX-like Family:IscX-like 2 c3ch0A_ 15.5 30 PDB header:hydrolase Chain: A: PDB Molecule:glycerophosphodiester phosphodiesterase; PDBTitle: crystal structure of glycerophosphoryl diester phosphodiesterase2 (yp_677622.1) from cytophaga hutchinsonii atcc 33406 at 1.50 a3 resolution 3 d1o1za_ 13.5 30 Fold:TIM beta/alpha-barrel Superfamily:PLC-like phosphodiesterases Family:Glycerophosphoryl diester phosphodiesterase 4 d1zcca1 10.5 30 Fold:TIM beta/alpha-barrel Superfamily:PLC-like phosphodiesterases Family:Glycerophosphoryl diester phosphodiesterase 5 c2pz0B_ 9.6 35 PDB header:hydrolase Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis 6 c2otdC_ 9.3 43 PDB header:hydrolase Chain: C: PDB Molecule:glycerophosphodiester phosphodiesterase; PDBTitle: the crystal structure of the glycerophosphodiester phosphodiesterase2 from shigella flexneri 2a 7 c3i10A_ 8.1 26 PDB header:hydrolase Chain: A: PDB Molecule:putative glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (np_812074.1) from bacteroides thetaiotaomicron3 vpi-5482 at 1.35 a resolution 8 d1ydya1 8.0 35 Fold:TIM beta/alpha-barrel Superfamily:PLC-like phosphodiesterases Family:Glycerophosphoryl diester phosphodiesterase 9 c1ydyA_ 8.0 35 PDB header:hydrolase Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of periplasmic glycerophosphodiester2 phosphodiesterase from escherichia coli 10 c3mz2A_ 8.0 26 PDB header:hydrolase Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of a glycerophosphoryl diester phosphodiesterase2 (bdi_3922) from parabacteroides distasonis atcc 8503 at 1.55 a3 resolution 11 c3mstA_ 7.8 50 PDB header:transport protein Chain: A: PDB Molecule:putative nitrate transport protein; PDBTitle: crystal structure of a putative nitrate transport protein (tvn0104)2 from thermoplasma volcanium at 1.35 a resolution 12 d1vd6a1 7.5 22 Fold:TIM beta/alpha-barrel Superfamily:PLC-like phosphodiesterases Family:Glycerophosphoryl diester phosphodiesterase 13 c2p76H_ 6.6 44 PDB header:hydrolase Chain: H: PDB Molecule:glycerophosphoryl diester phosphodiesterase; PDBTitle: crystal structure of a glycerophosphodiester phosphodiesterase from2 staphylococcus aureus 14 d1whga_ 6.3 27 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 15 d1koha2 5.6 38 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Non-canonical RBD 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