Phyre 2 Results for P0AEY1

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Email | l.a.kelley@imperial.ac.uk
Description | P0AEY1
Date | Thu Jan 5 11:24:35 GMT 2012
Unique Job ID | bb022393da07d744

Summary |

Top model
Image coloured by rainbow N → C terminus
| Close Jmol

Model (left) based on template c3aqpB_
Top template information
PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus
Confidence and coverage
Confidence: | 54.4% | Coverage: | 61%
134 residues ( 61% of your sequence) have been modelled with 54.4% 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 | L | D | L | F | K | A | I | G | L | G | L | V | V | L | L | P | L | A | N | P | L | T | T | V | A | L | F | L | G | L | A | G | N | M | N | S | A | E | R | N | R | Q | S | L | M | A | S | V | Y | V | F | A | I | M | M | V | A | Y | Y
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | A | G | Q | L | V | M | D | T | F | G | I | S | I | P | G | L | R | I | A | G | G | L | I | V | A | F | I | G | F | R | M | L | F | P | Q | Q | K | A | I | D | S | P | E | A | K | S | K | S | E | E | L | E | D | E | P | S | A | N | I | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | F | V | P | L | A | M | P | S | T | A | G | P | G | T | I | A | M | I | I | S | S | A | S | T | V | R | Q | S | S | T | F | A | D | W | V | L | M | V | A | P | P | L | I | F | F | L | V | A | V | I | L | W | G | S | L | R | S | S | G | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | .
Sequence |  | I | M | R | L | V | G | K | G | G | I | E | A | I | S | R | L | M | G | F | L | L | V | C | M | G | V | Q | F | I | I | N | G | I | L | E | I | I | K | T | Y | H
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 |
| c3aqpB_ |

### PDB 3aqp chain B

Region: 45 - 184
Aligned: 134
Modelled: 140
Confidence: 54.4%
Identity: 9%
PDB header:membrane protein
Chain: B: PDB Molecule:probable secdf protein-export membrane protein;
PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus

Phyre2
2 |
| c3k07A_ |

### PDB 3k07 chain A

Region: 45 - 191
Aligned: 145
Modelled: 147
Confidence: 51.3%
Identity: 8%
PDB header:transport protein
Chain: A: PDB Molecule:cation efflux system protein cusa;
PDBTitle: crystal structure of cusa

Phyre2
3 |
| c1oy8A_ |

### PDB 1oy8 chain A

Region: 45 - 90
Aligned: 46
Modelled: 46
Confidence: 27.7%
Identity: 20%
PDB header:membrane protein
Chain: A: PDB Molecule:acriflavine resistance protein b;
PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump

Phyre2
4 |
| c2vv5D_ |

### PDB 2vv5 chain D

Region: 6 - 91
Aligned: 86
Modelled: 86
Confidence: 18.3%
Identity: 6%
PDB header:membrane protein
Chain: D: PDB Molecule:small-conductance mechanosensitive channel;
PDBTitle: the open structure of mscs

Phyre2
5 |
| c1hjiB_ |

### PDB 1hji chain B

Region: 33 - 54
Aligned: 22
Modelled: 22
Confidence: 14.7%
Identity: 18%
PDB header:bacteriophage hk022
Chain: B: PDB Molecule:nun-protein;
PDBTitle: bacteriophage hk022 nun-protein-nutboxb-rna complex

Phyre2
6 |
| d2nn6h3 |

### PDB 2nn6 chain H domain 3

Region: 33 - 74
Aligned: 42
Modelled: 42
Confidence: 7.6%
Identity: 12%
Fold: Eukaryotic type KH-domain (KH-domain type I)
Superfamily: Eukaryotic type KH-domain (KH-domain type I)
Family: Eukaryotic type KH-domain (KH-domain type I)

Phyre2
7 |
| d2vv5a3 |

### PDB 2vv5 chain A domain 3

Region: 37 - 91
Aligned: 55
Modelled: 55
Confidence: 6.4%
Identity: 5%
Fold: Mechanosensitive channel protein MscS (YggB), transmembrane region
Superfamily: Mechanosensitive channel protein MscS (YggB), transmembrane region
Family: Mechanosensitive channel protein MscS (YggB), transmembrane region

Phyre2
8 |
| d1iwga8 |

### PDB 1iwg chain A domain 8

Region: 45 - 171
Aligned: 124
Modelled: 127
Confidence: 6.1%
Identity: 8%
Fold: Multidrug efflux transporter AcrB transmembrane domain
Superfamily: Multidrug efflux transporter AcrB transmembrane domain
Family: Multidrug efflux transporter AcrB transmembrane domain

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3aqpB_ |
|  | 54.4 | 9 | PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus
2 | c3k07A_ |
|  | 51.3 | 8 | PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa
3 | c1oy8A_ |
|  | 27.7 | 20 | PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump
4 | c2vv5D_ |
|  | 18.3 | 6 | PDB header:membrane protein Chain: D: PDB Molecule:small-conductance mechanosensitive channel; PDBTitle: the open structure of mscs
5 | c1hjiB_ |
|  | 14.7 | 18 | PDB header:bacteriophage hk022 Chain: B: PDB Molecule:nun-protein; PDBTitle: bacteriophage hk022 nun-protein-nutboxb-rna complex
6 | d2nn6h3 |
|  | 7.6 | 12 | Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I)
7 | d2vv5a3 |
|  | 6.4 | 5 | Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region Family:Mechanosensitive channel protein MscS (YggB), transmembrane region
8 | d1iwga8 |
|  | 6.1 | 8 | Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain

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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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