Phyre 2 Results for P11289

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Email | l.a.kelley@imperial.ac.uk
Description | P11289
Date | Thu Jan 5 11:32:32 GMT 2012
Unique Job ID | 87303bd1c7a2df11

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2jrmA_
Top template information
PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55
Confidence and coverage
Confidence: | 68.1% | Coverage: | 32%
39 residues ( 32% of your sequence) have been modelled with 68.1% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | M | K | K | F | I | A | P | L | L | A | L | L | V | S | G | C | Q | I | D | P | Y | T | H | A | P | T | L | T | S | T | D | W | Y | D | V | G | M | E | D | A | I | S | G | S | A | I | K | D | D | D | A | F | S | D | S | Q | A | D | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  | ? | ? |  |  |  |  | ? | ? |  | ? | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | G | L | Y | L | K | G | Y | A | E | G | Q | K | K | T | C | Q | T | D | F | T | Y | A | R | G | L | S | G | K | S | F | P | A | S | C | N | N | V | E | N | A | S | Q | L | H | E | V | W | Q | K | G | A | D | E | N | A | S | T | I | R | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  | ? | ? | ? | ? | ? | ? |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | .
Sequence |  | N
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 |
| c2jrmA_ |

### PDB 2jrm chain A

Region: 34 - 74
Aligned: 39
Modelled: 41
Confidence: 68.1%
Identity: 15%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:ribosome modulation factor;
PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55

Phyre2
2 |
| c2ae3A_ |

### PDB 2ae3 chain A

Region: 44 - 74
Aligned: 31
Modelled: 31
Confidence: 11.9%
Identity: 16%
PDB header:hydrolase
Chain: A: PDB Molecule:glutaryl 7-aminocephalosporanic acid acylase;
PDBTitle: glutaryl 7-aminocephalosporanic acid acylase: mutational study of2 activation mechanism

Phyre2
3 |
| c2khgA_ |

### PDB 2khg chain A

Region: 37 - 49
Aligned: 13
Modelled: 13
Confidence: 7.5%
Identity: 38%
PDB header:antimicrobial protein
Chain: A: PDB Molecule:plnj;
PDBTitle: plantaricin j in tfe

Phyre2
4 |
| d2ijra1 |

### PDB 2ijr chain A domain 1

Region: 3 - 30
Aligned: 26
Modelled: 26
Confidence: 6.8%
Identity: 15%
Fold: Api92-like
Superfamily: Api92-like
Family: Api92-like

Phyre2
5 |
| c2wybA_ |

### PDB 2wyb chain A

Region: 44 - 74
Aligned: 31
Modelled: 31
Confidence: 6.0%
Identity: 16%
PDB header:hydrolase
Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit
PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid

Phyre2
6 |
| d2fxta1 |

### PDB 2fxt chain A domain 1

Region: 60 - 82
Aligned: 22
Modelled: 23
Confidence: 5.6%
Identity: 23%
Fold: Cystatin-like
Superfamily: NTF2-like
Family: TIM44-like

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2jrmA_ |
|  | 68.1 | 15 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55
2 | c2ae3A_ |
|  | 11.9 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:glutaryl 7-aminocephalosporanic acid acylase; PDBTitle: glutaryl 7-aminocephalosporanic acid acylase: mutational study of2 activation mechanism
3 | c2khgA_ |
|  | 7.5 | 38 | PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in tfe
4 | d2ijra1 |
|  | 6.8 | 15 | Fold:Api92-like Superfamily:Api92-like Family:Api92-like
5 | c2wybA_ |
|  | 6.0 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid
6 | d2fxta1 |
|  | 5.6 | 23 | Fold:Cystatin-like Superfamily:NTF2-like Family:TIM44-like

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