Secondary structure and disorder prediction

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10

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20

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40

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Sequence

M

S

K

K

L

A

K

K

R

Q

P

V

K

P

V

V

A

K

E

P

A

R

T

A

K

N

F

G

Y

E

E

M

L

S

E

L

E

A

I

V

A

D

A

E

T

R

L

A

E

D

E

A

T

A

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 1vp7 chain B Region: 19 - 44 Aligned: 26 Modelled: 24 Confidence: 55.7% Identity: 27% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 1vp7 chain A Region: 29 - 44 Aligned: 16 Modelled: 14 Confidence: 35.2% Identity: 44% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 1vp7 chain D Region: 29 - 49 Aligned: 21 Modelled: 21 Confidence: 28.0% Identity: 38% PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution Phyre2 PDB 2ca1 chain A domain 1 Region: 1 - 35 Aligned: 34 Modelled: 35 Confidence: 23.6% Identity: 24% Fold: Nucleocapsid protein dimerization domain Superfamily: Nucleocapsid protein dimerization domain Family: Coronavirus nucleocapsid protein Phyre2 PDB 2cjr chain A domain 1 Region: 1 - 35 Aligned: 35 Modelled: 35 Confidence: 21.9% Identity: 31% Fold: Nucleocapsid protein dimerization domain Superfamily: Nucleocapsid protein dimerization domain Family: Coronavirus nucleocapsid protein Phyre2 PDB 3ayh chain A Region: 33 - 51 Aligned: 19 Modelled: 19 Confidence: 16.4% Identity: 32% PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase iii subunit rpc9; PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii Phyre2 PDB 2omd chain B Region: 29 - 46 Aligned: 18 Modelled: 18 Confidence: 10.9% Identity: 33% PDB header:lyase Chain: B: PDB Molecule:molybdopterin-converting factor subunit 2; PDBTitle: crystal structure of molybdopterin converting factor subunit 22 (aq_2181) from aquifex aeolicus vf5 Phyre2 PDB 1ni8 chain A Region: 30 - 42 Aligned: 13 Modelled: 13 Confidence: 9.4% Identity: 54% Fold: H-NS histone-like proteins Superfamily: H-NS histone-like proteins Family: H-NS histone-like proteins Phyre2 PDB 2kkr chain A Region: 21 - 38 Aligned: 18 Modelled: 18 Confidence: 8.8% Identity: 17% PDB header:transcription, protein binding Chain: A: PDB Molecule:ataxin-7; PDBTitle: solution structure of sca7 zinc finger domain from human ataxin-72 protein Phyre2 PDB 3bux chain B domain 2 Region: 26 - 43 Aligned: 18 Modelled: 18 Confidence: 7.2% Identity: 28% Fold: N-cbl like Superfamily: N-terminal domain of cbl (N-cbl) Family: N-terminal domain of cbl (N-cbl) Phyre2 PDB 1rr7 chain A Region: 29 - 54 Aligned: 26 Modelled: 26 Confidence: 7.0% Identity: 27% PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu Phyre2 PDB 1rr7 chain A Region: 29 - 54 Aligned: 26 Modelled: 26 Confidence: 7.0% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Middle operon regulator, Mor Phyre2 PDB 1oqe chain N Region: 12 - 19 Aligned: 8 Modelled: 8 Confidence: 6.9% Identity: 38% Fold: TNF receptor-like Superfamily: TNF receptor-like Family: BAFF receptor-like Phyre2 PDB 1lr1 chain A Region: 30 - 42 Aligned: 13 Modelled: 13 Confidence: 6.4% Identity: 54% Fold: H-NS histone-like proteins Superfamily: H-NS histone-like proteins Family: H-NS histone-like proteins Phyre2 1 d1vp7b_ 2 d1vp7a_ 3 c1vp7D_ 4 d2ca1a1 5 d2cjra1 6 c3ayhA_ 7 c2omdB_ 8 d1ni8a_ 9 c2kkrA_ 10 d3buxb2 11 c1rr7A_ 12 d1rr7a_ 13 d1oqen_ 14 d1lr1a_

Detailed template information

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

1 d1vp7b_ 55.7 27 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 2 d1vp7a_ 35.2 44 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 3 c1vp7D_ 28.0 38 PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution 4 d2ca1a1 23.6 24 Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Coronavirus nucleocapsid protein 5 d2cjra1 21.9 31 Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Coronavirus nucleocapsid protein 6 c3ayhA_ 16.4 32 PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase iii subunit rpc9; PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii 7 c2omdB_ 10.9 33 PDB header:lyase Chain: B: PDB Molecule:molybdopterin-converting factor subunit 2; PDBTitle: crystal structure of molybdopterin converting factor subunit 22 (aq_2181) from aquifex aeolicus vf5 8 d1ni8a_ 9.4 54 Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins 9 c2kkrA_ 8.8 17 PDB header:transcription, protein binding Chain: A: PDB Molecule:ataxin-7; PDBTitle: solution structure of sca7 zinc finger domain from human ataxin-72 protein 10 d3buxb2 7.2 28 Fold:N-cbl like Superfamily:N-terminal domain of cbl (N-cbl) Family:N-terminal domain of cbl (N-cbl) 11 c1rr7A_ 7.0 27 PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu 12 d1rr7a_ 7.0 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor 13 d1oqen_ 6.9 38 Fold:TNF receptor-like Superfamily:TNF receptor-like Family:BAFF receptor-like 14 d1lr1a_ 6.4 54 Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins

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