Phyre 2 Results for P27844

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P27844
Date | Thu Jan 5 11:44:19 GMT 2012
Unique Job ID | 83a8223a1e4eab78

Summary |

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

Model (left) based on template d1s7ba_
Top template information
Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE
Confidence and coverage
Confidence: | 97.8% | Coverage: | 25%
75 residues ( 25% of your sequence) have been modelled with 97.8% 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.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | D | A | K | Q | T | R | Q | G | V | L | L | A | L | A | A | Y | F | I | W | G | I | A | P | A | Y | F | K | L | I | Y | Y | V | P | A | D | E | I | L | T | H | R | V | I | W | S | F | F | F | M | V | V | L | M | S | I | C | R | Q | W
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | Y | L | K | T | L | I | Q | T | P | Q | K | I | F | M | L | A | V | S | A | V | L | I | G | G | N | W | L | L | F | I | W | A | V | N | N | H | H | M | L | E | A | S | L | G | Y | F | I | N | P | L | V | N | I | V | L | G | M | I | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | L | G | E | R | F | R | R | M | Q | W | L | A | V | I | L | A | I | C | G | V | L | V | Q | L | W | T | F | G | S | L | P | I | I | A | L | G | L | A | F | S | F | A | F | Y | G | L | V | R | K | K | I | A | V | E | A | Q | T | G | M | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | I | E | T | M | W | L | L | P | V | A | A | I | Y | L | F | A | I | A | D | S | S | T | S | H | M | G | Q | N | P | M | S | L | N | L | L | L | I | A | A | G | I | V | T | T | V | P | L | L | C | F | T | A | A | A | T | R | L | R | L | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | .
Sequence |  | T | L | G | F | F | Q | Y | I | G | P | T | L | M | F | L | L | A | V | T | F | Y | G | E | K | P | G | A | D | K | M | V | T | F | A | F | I | W | V | A | L | A | I | F | V | M | D | A | I | Y | T | Q | R | R | T | S | 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 |
| d1s7ba_ |

### PDB 1s7b chain A

Region: 218 - 292
Aligned: 75
Modelled: 75
Confidence: 97.8%
Identity: 13%
Fold: Multidrug resistance efflux transporter EmrE
Superfamily: Multidrug resistance efflux transporter EmrE
Family: Multidrug resistance efflux transporter EmrE

Phyre2
2 |
| c2i68B_ |

### PDB 2i68 chain B

Region: 222 - 285
Aligned: 58
Modelled: 64
Confidence: 83.4%
Identity: 17%
PDB header:transport protein
Chain: B: PDB Molecule:protein emre;
PDBTitle: cryo-em based theoretical model structure of transmembrane2 domain of the multidrug-resistance antiporter from e. coli3 emre

Phyre2
3 |
| c3aqpB_ |

### PDB 3aqp chain B

Region: 209 - 296
Aligned: 87
Modelled: 88
Confidence: 68.6%
Identity: 14%
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
4 |
| d1iwga8 |

### PDB 1iwg chain A domain 8

Region: 215 - 296
Aligned: 82
Modelled: 82
Confidence: 30.0%
Identity: 17%
Fold: Multidrug efflux transporter AcrB transmembrane domain
Superfamily: Multidrug efflux transporter AcrB transmembrane domain
Family: Multidrug efflux transporter AcrB transmembrane domain

Phyre2
5 |
| c2jp3A_ |

### PDB 2jp3 chain A

Region: 270 - 296
Aligned: 27
Modelled: 27
Confidence: 15.9%
Identity: 7%
PDB header:transcription
Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4;
PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles

Phyre2
6 |
| c3rkoF_ |

### PDB 3rko chain F

Region: 3 - 150
Aligned: 142
Modelled: 148
Confidence: 14.8%
Identity: 11%
PDB header:oxidoreductase
Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j;
PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution

Phyre2
7 |
| c3giaA_ |

### PDB 3gia chain A

Region: 63 - 296
Aligned: 217
Modelled: 234
Confidence: 13.0%
Identity: 8%
PDB header:transport protein
Chain: A: PDB Molecule:uncharacterized protein mj0609;
PDBTitle: crystal structure of apct transporter

Phyre2
8 |
| c3lrcC_ |

### PDB 3lrc chain C

Region: 183 - 294
Aligned: 112
Modelled: 112
Confidence: 8.0%
Identity: 10%
PDB header:transport protein
Chain: C: PDB Molecule:arginine/agmatine antiporter;
PDBTitle: structure of e. coli adic (p1)

Phyre2
9 |
| c2mltB_ |

### PDB 2mlt chain B

Region: 271 - 295
Aligned: 25
Modelled: 25
Confidence: 7.1%
Identity: 4%
PDB header:toxin (hemolytic polypeptide)
Chain: B: PDB Molecule:melittin;
PDBTitle: melittin

Phyre2
10 |
| c2mltA_ |

### PDB 2mlt chain A

Region: 271 - 295
Aligned: 25
Modelled: 25
Confidence: 7.1%
Identity: 4%
PDB header:toxin (hemolytic polypeptide)
Chain: A: PDB Molecule:melittin;
PDBTitle: melittin

Phyre2
11 |
| c3hd6A_ |

### PDB 3hd6 chain A

Region: 45 - 231
Aligned: 187
Modelled: 187
Confidence: 6.7%
Identity: 12%
PDB header:membrane protein, transport protein
Chain: A: PDB Molecule:ammonium transporter rh type c;
PDBTitle: crystal structure of the human rhesus glycoprotein rhcg

Phyre2
12 |
| c2hg5D_ |

### PDB 2hg5 chain D

Region: 269 - 296
Aligned: 28
Modelled: 28
Confidence: 6.0%
Identity: 11%
PDB header:membrane protein
Chain: D: PDB Molecule:kcsa channel;
PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter

Phyre2
13 |
| c2kncB_ |

### PDB 2knc chain B

Region: 263 - 296
Aligned: 34
Modelled: 34
Confidence: 5.1%
Identity: 15%
PDB header:cell adhesion
Chain: B: PDB Molecule:integrin beta-3;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1s7ba_ |
|  | 97.8 | 13 | Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE
2 | c2i68B_ |
|  | 83.4 | 17 | PDB header:transport protein Chain: B: PDB Molecule:protein emre; PDBTitle: cryo-em based theoretical model structure of transmembrane2 domain of the multidrug-resistance antiporter from e. coli3 emre
3 | c3aqpB_ |
|  | 68.6 | 14 | 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
4 | d1iwga8 |
|  | 30.0 | 17 | Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain
5 | c2jp3A_ |
|  | 15.9 | 7 | PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles
6 | c3rkoF_ |
|  | 14.8 | 11 | PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution
7 | c3giaA_ |
|  | 13.0 | 8 | PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter
8 | c3lrcC_ |
|  | 8.0 | 10 | PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1)
9 | c2mltB_ |
|  | 7.1 | 4 | PDB header:toxin (hemolytic polypeptide) Chain: B: PDB Molecule:melittin; PDBTitle: melittin
10 | c2mltA_ |
|  | 7.1 | 4 | PDB header:toxin (hemolytic polypeptide) Chain: A: PDB Molecule:melittin; PDBTitle: melittin
11 | c3hd6A_ |
|  | 6.7 | 12 | PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg
12 | c2hg5D_ |
|  | 6.0 | 11 | PDB header:membrane protein Chain: D: PDB Molecule:kcsa channel; PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter
13 | c2kncB_ |
|  | 5.1 | 15 | PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

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
Disclaimer
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