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

G

D

D

V

H

R

F

G

N

L

F

L

I

S

P

S

S

N

S

I

L

S

N

Y

S

P

A

D

K

K

K

F

Y

V

E

T

E

R

A

E

S

P

K

Q

A

I

M

M

S

Y

K

E

W

G

P

D

G

Q

G

Secondary structure

SS confidence

Disorder

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?

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?

Disorder confidence

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70

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80

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Sequence

I

N

N

I

E

S

H

E

H

A

M

L

T

L

L

K

E

H

R

D

M

T

L

P

T

R

K

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 2juz chain A domain 1 Region: 57 - 78 Aligned: 22 Modelled: 22 Confidence: 22.5% Identity: 14% Fold: YejL-like Superfamily: YejL-like Family: YejL-like Phyre2 PDB 2qgp chain A Region: 6 - 35 Aligned: 30 Modelled: 30 Confidence: 20.4% Identity: 13% PDB header:hydrolase Chain: A: PDB Molecule:hnh endonuclease; PDBTitle: x-ray structure of the nhn endonuclease from geobacter2 metallireducens. northeast structural genomics consortium3 target gmr87. Phyre2 PDB 2rhf chain A Region: 57 - 80 Aligned: 24 Modelled: 24 Confidence: 20.0% Identity: 25% PDB header:hydrolase Chain: A: PDB Molecule:dna helicase recq; PDBTitle: d. radiodurans recq hrdc domain 3 Phyre2 PDB 2rrd chain A Region: 57 - 84 Aligned: 28 Modelled: 28 Confidence: 18.2% Identity: 21% PDB header:dna binding protein Chain: A: PDB Molecule:hrdc domain from bloom syndrome protein; PDBTitle: structure of hrdc domain from human bloom syndrome protein, blm Phyre2 PDB 1rqp chain A domain 1 Region: 6 - 13 Aligned: 8 Modelled: 8 Confidence: 17.8% Identity: 50% Fold: Bacterial fluorinating enzyme, C-terminal domain Superfamily: Bacterial fluorinating enzyme, C-terminal domain Family: Bacterial fluorinating enzyme, C-terminal domain Phyre2 PDB 2juw chain A domain 1 Region: 56 - 78 Aligned: 23 Modelled: 23 Confidence: 15.7% Identity: 22% Fold: YejL-like Superfamily: YejL-like Family: YejL-like Phyre2 PDB 2jrx chain A domain 1 Region: 57 - 78 Aligned: 22 Modelled: 22 Confidence: 15.3% Identity: 18% Fold: YejL-like Superfamily: YejL-like Family: YejL-like Phyre2 PDB 2jpq chain A domain 1 Region: 56 - 78 Aligned: 23 Modelled: 23 Confidence: 15.1% Identity: 13% Fold: YejL-like Superfamily: YejL-like Family: YejL-like Phyre2 PDB 3khz chain A Region: 61 - 77 Aligned: 17 Modelled: 17 Confidence: 7.5% Identity: 18% PDB header:hydrolase Chain: A: PDB Molecule:putative dipeptidase sacol1801; PDBTitle: crystal structure of r350a mutant of staphylococcus aureus2 metallopeptidase (sapep/dape) in the apo-form Phyre2 PDB 1wud chain A domain 1 Region: 57 - 80 Aligned: 24 Modelled: 24 Confidence: 7.4% Identity: 25% Fold: SAM domain-like Superfamily: HRDC-like Family: HRDC domain from helicases Phyre2 1 d2juza1 2 c2qgpA_ 3 c2rhfA_ 4 c2rrdA_ 5 d1rqpa1 6 d2juwa1 7 d2jrxa1 8 d2jpqa1 9 c3khzA_ 10 d1wuda1

Detailed template information

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

1 d2juza1 22.5 14 Fold:YejL-like Superfamily:YejL-like Family:YejL-like 2 c2qgpA_ 20.4 13 PDB header:hydrolase Chain: A: PDB Molecule:hnh endonuclease; PDBTitle: x-ray structure of the nhn endonuclease from geobacter2 metallireducens. northeast structural genomics consortium3 target gmr87. 3 c2rhfA_ 20.0 25 PDB header:hydrolase Chain: A: PDB Molecule:dna helicase recq; PDBTitle: d. radiodurans recq hrdc domain 3 4 c2rrdA_ 18.2 21 PDB header:dna binding protein Chain: A: PDB Molecule:hrdc domain from bloom syndrome protein; PDBTitle: structure of hrdc domain from human bloom syndrome protein, blm 5 d1rqpa1 17.8 50 Fold:Bacterial fluorinating enzyme, C-terminal domain Superfamily:Bacterial fluorinating enzyme, C-terminal domain Family:Bacterial fluorinating enzyme, C-terminal domain 6 d2juwa1 15.7 22 Fold:YejL-like Superfamily:YejL-like Family:YejL-like 7 d2jrxa1 15.3 18 Fold:YejL-like Superfamily:YejL-like Family:YejL-like 8 d2jpqa1 15.1 13 Fold:YejL-like Superfamily:YejL-like Family:YejL-like 9 c3khzA_ 7.5 18 PDB header:hydrolase Chain: A: PDB Molecule:putative dipeptidase sacol1801; PDBTitle: crystal structure of r350a mutant of staphylococcus aureus2 metallopeptidase (sapep/dape) in the apo-form 10 d1wuda1 7.4 25 Fold:SAM domain-like Superfamily:HRDC-like Family:HRDC domain from helicases

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