Phyre 2 Results for P0AAW9

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P0AAW9
Date | Wed Jan 25 15:20:21 GMT 2012
Unique Job ID | b9c036eb9d2f65e9

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2ajmA_
Top template information
PDB header:membrane protein Chain: A: PDB Molecule:nonstructural protein 5a; PDBTitle: nmr structure of the in-plane membrane anchor domain [1-28]2 of the monotopic nonstructural protein 5a (ns5a) from the3 bovine viral diarrhea virus (bvdv)
Confidence and coverage
Confidence: | 23.7% | Coverage: | 27%
13 residues ( 27% of your sequence) have been modelled with 23.7% 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
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Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | L | E | L | L | K | S | L | V | F | A | V | I | M | V | P | V | V | M | A | I | I | L | G | L | I | Y | G | L | G | E | V | F | N | I | F | S | G | V | G | K | K | D | Q | P | G | Q | N | H
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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 |
| c2ajmA_ |

### PDB 2ajm chain A

Region: 22 - 34
Aligned: 13
Modelled: 13
Confidence: 23.7%
Identity: 46%
PDB header:membrane protein
Chain: A: PDB Molecule:nonstructural protein 5a;
PDBTitle: nmr structure of the in-plane membrane anchor domain [1-28]2 of the monotopic nonstructural protein 5a (ns5a) from the3 bovine viral diarrhea virus (bvdv)

Phyre2
2 |
| c3dinD_ |

### PDB 3din chain D

Region: 3 - 36
Aligned: 34
Modelled: 34
Confidence: 19.6%
Identity: 21%
PDB header:membrane protein, protein transport
Chain: D: PDB Molecule:preprotein translocase subunit sece;
PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase

Phyre2
3 |
| d1jb0i_ |

### PDB 1jb0 chain I

Region: 12 - 29
Aligned: 18
Modelled: 18
Confidence: 7.9%
Identity: 33%
Fold: Single transmembrane helix
Superfamily: Subunit VIII of photosystem I reaction centre, PsaI
Family: Subunit VIII of photosystem I reaction centre, PsaI

Phyre2
4 |
| c3g79A_ |

### PDB 3g79 chain A

Region: 38 - 49
Aligned: 12
Modelled: 12
Confidence: 7.3%
Identity: 25%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ndp-n-acetyl-d-galactosaminuronic acid dehydrogenase;
PDBTitle: crystal structure of ndp-n-acetyl-d-galactosaminuronic acid2 dehydrogenase from methanosarcina mazei go1

Phyre2
5 |
| c1afoB_ |

### PDB 1afo chain B

Region: 16 - 37
Aligned: 22
Modelled: 22
Confidence: 6.4%
Identity: 27%
PDB header:integral membrane protein
Chain: B: PDB Molecule:glycophorin a;
PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures

Phyre2
6 |
| c2kv5A_ |

### PDB 2kv5 chain A

Region: 5 - 22
Aligned: 18
Modelled: 18
Confidence: 6.0%
Identity: 50%
PDB header:toxin
Chain: A: PDB Molecule:putative uncharacterized protein rnai;
PDBTitle: solution structure of the par toxin fst in dpc micelles

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2ajmA_ |
|  | 23.7 | 46 | PDB header:membrane protein Chain: A: PDB Molecule:nonstructural protein 5a; PDBTitle: nmr structure of the in-plane membrane anchor domain [1-28]2 of the monotopic nonstructural protein 5a (ns5a) from the3 bovine viral diarrhea virus (bvdv)
2 | c3dinD_ |
|  | 19.6 | 21 | PDB header:membrane protein, protein transport Chain: D: PDB Molecule:preprotein translocase subunit sece; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase
3 | d1jb0i_ |
|  | 7.9 | 33 | Fold:Single transmembrane helix Superfamily:Subunit VIII of photosystem I reaction centre, PsaI Family:Subunit VIII of photosystem I reaction centre, PsaI
4 | c3g79A_ |
|  | 7.3 | 25 | PDB header:oxidoreductase Chain: A: PDB Molecule:ndp-n-acetyl-d-galactosaminuronic acid dehydrogenase; PDBTitle: crystal structure of ndp-n-acetyl-d-galactosaminuronic acid2 dehydrogenase from methanosarcina mazei go1
5 | c1afoB_ |
|  | 6.4 | 27 | PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures
6 | c2kv5A_ |
|  | 6.0 | 50 | PDB header:toxin Chain: A: PDB Molecule:putative uncharacterized protein rnai; PDBTitle: solution structure of the par toxin fst in dpc micelles

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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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