Phyre 2 Results for P77519

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Email | l.a.kelley@imperial.ac.uk
Description | P77519
Date | Thu Jan 5 12:30:12 GMT 2012
Unique Job ID | 7a3e5e5438b12715

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1osma_
Top template information
Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin
Confidence and coverage
Confidence: | 99.8% | Coverage: | 74%
71 residues ( 74% of your sequence) have been modelled with 99.8% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | K | L | K | I | V | A | V | V | V | T | G | L | L | A | A | N | V | A | H | A | A | E | V | Y | N | K | D | G | N | K | L | D | L | Y | G | K | V | T | A | L | R | Y | F | T | D | D | K | R | D | D | G | D | K | T | Y | A | R | L | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | .
Sequence |  | F | K | G | E | T | Q | I | N | D | Q | M | I | G | F | G | H | W | E | Y | D | F | K | G | Y | N | D | E | A | N | G | S | R | G | K | N | L
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 |
| d1osma_ |

### PDB 1osm chain A

Region: 22 - 92
Aligned: 71
Modelled: 71
Confidence: 99.8%
Identity: 63%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2
2 |
| d1phoa_ |

### PDB 1pho chain A

Region: 22 - 92
Aligned: 71
Modelled: 71
Confidence: 99.8%
Identity: 58%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2
3 |
| c3nsgA_ |

### PDB 3nsg chain A

Region: 23 - 93
Aligned: 71
Modelled: 71
Confidence: 99.8%
Identity: 51%
PDB header:membrane protein
Chain: A: PDB Molecule:outer membrane protein f;
PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi

Phyre2
4 |
| d2zfga1 |

### PDB 2zfg chain A domain 1

Region: 22 - 94
Aligned: 73
Modelled: 73
Confidence: 99.8%
Identity: 58%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2
5 |
| d2fgqx1 |

### PDB 2fgq chain X domain 1

Region: 31 - 95
Aligned: 65
Modelled: 65
Confidence: 99.6%
Identity: 20%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2
6 |
| c3a2rX_ |

### PDB 3a2r chain X

Region: 32 - 94
Aligned: 63
Modelled: 63
Confidence: 99.6%
Identity: 17%
PDB header:membrane protein
Chain: X: PDB Molecule:outer membrane protein ii;
PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis

Phyre2
7 |
| d3prna_ |

### PDB 3prn chain A

Region: 32 - 94
Aligned: 63
Modelled: 63
Confidence: 99.2%
Identity: 13%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2
8 |
| d2pora_ |

### PDB 2por chain A

Region: 32 - 91
Aligned: 58
Modelled: 60
Confidence: 99.2%
Identity: 10%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2
9 |
| c2o4vA_ |

### PDB 2o4v chain A

Region: 26 - 88
Aligned: 61
Modelled: 63
Confidence: 90.1%
Identity: 23%
PDB header:membrane protein
Chain: A: PDB Molecule:porin p;
PDBTitle: an arginine ladder in oprp mediates phosphate specific transfer across2 the outer membrane

Phyre2
10 |
| c2iwvD_ |

### PDB 2iwv chain D

Region: 30 - 90
Aligned: 61
Modelled: 61
Confidence: 71.6%
Identity: 11%
PDB header:ion channel
Chain: D: PDB Molecule:outer membrane protein g;
PDBTitle: structure of the monomeric outer membrane porin ompg in the2 open and closed conformation

Phyre2
11 |
| d2jnaa1 |

### PDB 2jna chain A domain 1

Region: 1 - 24
Aligned: 24
Modelled: 24
Confidence: 62.9%
Identity: 25%
Fold: Dodecin subunit-like
Superfamily: YdgH-like
Family: YdgH-like

Phyre2
12 |
| d1uynx_ |

### PDB 1uyn chain X

Region: 29 - 84
Aligned: 56
Modelled: 56
Confidence: 11.3%
Identity: 14%
Fold: Transmembrane beta-barrels
Superfamily: Autotransporter
Family: Autotransporter

Phyre2
13 |
| c2wjqA_ |

### PDB 2wjq chain A

Region: 58 - 95
Aligned: 38
Modelled: 38
Confidence: 10.1%
Identity: 13%
PDB header:transport protein
Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel
PDBTitle: nanc porin structure in hexagonal crystal form.

Phyre2
14 |
| c2vdaB_ |

### PDB 2vda chain B

Region: 2 - 21
Aligned: 20
Modelled: 20
Confidence: 9.9%
Identity: 25%
PDB header:protein transport
Chain: B: PDB Molecule:maltoporin;
PDBTitle: solution structure of the seca-signal peptide complex

Phyre2
15 |
| c2jwyA_ |

### PDB 2jwy chain A

Region: 36 - 80
Aligned: 40
Modelled: 45
Confidence: 6.4%
Identity: 23%
PDB header:lipoprotein
Chain: A: PDB Molecule:uncharacterized lipoprotein yaji;
PDBTitle: solution nmr structure of uncharacterized lipoprotein yaji from2 escherichia coli. northeast structural genomics target er540

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1osma_ |
|  | 99.8 | 63 | Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin
2 | d1phoa_ |
|  | 99.8 | 58 | Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin
3 | c3nsgA_ |
|  | 99.8 | 51 | PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein f; PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi
4 | d2zfga1 |
|  | 99.8 | 58 | Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin
5 | d2fgqx1 |
|  | 99.6 | 20 | Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin
6 | c3a2rX_ |
|  | 99.6 | 17 | PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis
7 | d3prna_ |
|  | 99.2 | 13 | Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin
8 | d2pora_ |
|  | 99.2 | 10 | Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin
9 | c2o4vA_ |
|  | 90.1 | 23 | PDB header:membrane protein Chain: A: PDB Molecule:porin p; PDBTitle: an arginine ladder in oprp mediates phosphate specific transfer across2 the outer membrane
10 | c2iwvD_ |
|  | 71.6 | 11 | PDB header:ion channel Chain: D: PDB Molecule:outer membrane protein g; PDBTitle: structure of the monomeric outer membrane porin ompg in the2 open and closed conformation
11 | d2jnaa1 |
|  | 62.9 | 25 | Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like
12 | d1uynx_ |
|  | 11.3 | 14 | Fold:Transmembrane beta-barrels Superfamily:Autotransporter Family:Autotransporter
13 | c2wjqA_ |
|  | 10.1 | 13 | PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form.
14 | c2vdaB_ |
|  | 9.9 | 25 | PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex
15 | c2jwyA_ |
|  | 6.4 | 23 | PDB header:lipoprotein Chain: A: PDB Molecule:uncharacterized lipoprotein yaji; PDBTitle: solution nmr structure of uncharacterized lipoprotein yaji from2 escherichia coli. northeast structural genomics target er540

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