Phyre 2 Results for P56976

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P56976
Date | Thu Jan 5 12:06:26 GMT 2012
Unique Job ID | 3d58b031b986fe63

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1sr3a_
Top template information
Fold:OB-fold Superfamily:Heme chaperone CcmE Family:Heme chaperone CcmE
Confidence and coverage
Confidence: | 14.9% | Coverage: | 41%
17 residues ( 41% of your sequence) have been modelled with 14.9% confidence by the single highest scoring template.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | N | R | L | I | E | L | T | G | W | I | V | L | V | V | S | V | I | L | L | G | V | A | S | H | I | D | N | Y | Q | P | P | E | Q | S | A | S | V | Q | H | K
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 |
| d1sr3a_ |

### PDB 1sr3 chain A

Region: 22 - 38
Aligned: 17
Modelled: 17
Confidence: 14.9%
Identity: 41%
Fold: OB-fold
Superfamily: Heme chaperone CcmE
Family: Heme chaperone CcmE

Phyre2
2 |
| c3o0rC_ |

### PDB 3o0r chain C

Region: 1 - 25
Aligned: 25
Modelled: 25
Confidence: 12.8%
Identity: 20%
PDB header:immune system/oxidoreductase
Chain: C: PDB Molecule:nitric oxide reductase subunit c;
PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment

Phyre2
3 |
| d2apla1 |

### PDB 2apl chain A domain 1

Region: 5 - 15
Aligned: 11
Modelled: 11
Confidence: 9.5%
Identity: 64%
Fold: PG0816-like
Superfamily: PG0816-like
Family: PG0816-like

Phyre2
4 |
| c3ke2A_ |

### PDB 3ke2 chain A

Region: 3 - 10
Aligned: 8
Modelled: 7
Confidence: 7.7%
Identity: 50%
PDB header:unknown function
Chain: A: PDB Molecule:uncharacterized protein yp_928783.1;
PDBTitle: crystal structure of a duf2131 family protein (sama_2911) from2 shewanella amazonensis sb2b at 2.50 a resolution

Phyre2
5 |
| d1h6ga2 |

### PDB 1h6g chain A domain 2

Region: 4 - 38
Aligned: 35
Modelled: 35
Confidence: 5.4%
Identity: 29%
Fold: Four-helical up-and-down bundle
Superfamily: alpha-catenin/vinculin-like
Family: alpha-catenin/vinculin

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1sr3a_ |
|  | 14.9 | 41 | Fold:OB-fold Superfamily:Heme chaperone CcmE Family:Heme chaperone CcmE
2 | c3o0rC_ |
|  | 12.8 | 20 | PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment
3 | d2apla1 |
|  | 9.5 | 64 | Fold:PG0816-like Superfamily:PG0816-like Family:PG0816-like
4 | c3ke2A_ |
|  | 7.7 | 50 | PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein yp_928783.1; PDBTitle: crystal structure of a duf2131 family protein (sama_2911) from2 shewanella amazonensis sb2b at 2.50 a resolution
5 | d1h6ga2 |
|  | 5.4 | 29 | Fold:Four-helical up-and-down bundle Superfamily:alpha-catenin/vinculin-like Family:alpha-catenin/vinculin

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

Transmembrane helix prediction |

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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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