Phyre 2 Results for P0ADB4

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P0ADB4
Date | Thu Jan 5 11:20:31 GMT 2012
Unique Job ID | 02548d1c05665d08

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d2rh3a1
Top template information
Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VirC2-like
Confidence and coverage
Confidence: | 25.9% | Coverage: | 71%
29 residues ( 71% of your sequence) have been modelled with 25.9% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | .
Sequence |  | M | M | K | R | L | I | V | L | V | L | L | A | S | T | L | L | T | G | C | N | T | A | R | G | F | G | E | D | I | K | H | L | G | N | S | I | S | R | A | A | 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
--- | ---
1 |
| d2rh3a1 |

### PDB 2rh3 chain A domain 1

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 25.9%
Identity: 24%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: VirC2-like

Phyre2
2 |
| c1pyvA_ |

### PDB 1pyv chain A

Region: 10 - 41
Aligned: 30
Modelled: 32
Confidence: 11.6%
Identity: 50%
PDB header:hydrolase
Chain: A: PDB Molecule:atp synthase beta chain, mitochondrial precursor;
PDBTitle: nmr solution structure of the mitochondrial f1b presequence2 peptide from nicotiana plumbaginifolia

Phyre2
3 |
| d1sp8a2 |

### PDB 1sp8 chain A domain 2

Region: 18 - 38
Aligned: 21
Modelled: 21
Confidence: 9.0%
Identity: 38%
Fold: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family: Extradiol dioxygenases

Phyre2
4 |
| c1debA_ |

### PDB 1deb chain A

Region: 20 - 36
Aligned: 17
Modelled: 17
Confidence: 7.4%
Identity: 35%
PDB header:structural protein
Chain: A: PDB Molecule:adenomatous polyposis coli protein;
PDBTitle: crystal structure of the n-terminal coiled coil domain from2 apc

Phyre2
5 |
| d1nh9a_ |

### PDB 1nh9 chain A

Region: 33 - 39
Aligned: 7
Modelled: 7
Confidence: 6.7%
Identity: 43%
Fold: IF3-like
Superfamily: AlbA-like
Family: DNA-binding protein AlbA

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2rh3a1 |
|  | 25.9 | 24 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VirC2-like
2 | c1pyvA_ |
|  | 11.6 | 50 | PDB header:hydrolase Chain: A: PDB Molecule:atp synthase beta chain, mitochondrial precursor; PDBTitle: nmr solution structure of the mitochondrial f1b presequence2 peptide from nicotiana plumbaginifolia
3 | d1sp8a2 |
|  | 9.0 | 38 | Fold:Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Superfamily:Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Family:Extradiol dioxygenases
4 | c1debA_ |
|  | 7.4 | 35 | PDB header:structural protein Chain: A: PDB Molecule:adenomatous polyposis coli protein; PDBTitle: crystal structure of the n-terminal coiled coil domain from2 apc
5 | d1nh9a_ |
|  | 6.7 | 43 | Fold:IF3-like Superfamily:AlbA-like Family:DNA-binding protein AlbA

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

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
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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