Phyre 2 Results for Q46841

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Email | l.a.kelley@imperial.ac.uk
Description | Q46841
Date | Wed Jan 25 15:21:13 GMT 2012
Unique Job ID | c4b48b8fce851435

Summary |

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

Model (left) based on template c3mkuA_
Top template information
PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter
Confidence and coverage
Confidence: | 100.0% | Coverage: | 98%
347 residues ( 98% of your sequence) have been modelled with 100.0% 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 | A | G | F | N | I | K | H | W | F | A | D | G | A | F | R | T | I | I | R | N | S | A | W | L | G | S | S | N | V | V | S | A | L | L | G | L | L | A | L | S | C | A | G | K | G | M | T | P | A | M | F | G | V | L | V | I | V | Q | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Y | A | K | S | I | S | D | F | I | K | F | Q | T | W | Q | L | V | V | Q | Y | G | T | P | A | L | T | N | N | N | P | Q | Q | F | R | N | V | V | S | F | S | F | S | L | D | I | V | S | G | A | V | A | I | V | G | G | I | A | L | L | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | F | L | S | H | S | L | G | L | D | D | Q | S | F | W | L | A | A | L | Y | C | T | L | I | P | S | M | A | S | S | T | P | T | G | I | L | R | A | V | D | R | F | D | L | I | A | V | Q | Q | A | T | K | P | F | L | R | A | A | G | S | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | V | A | W | Y | F | D | F | G | F | A | G | F | V | I | A | W | Y | V | S | N | L | V | G | G | T | M | Y | W | W | F | A | A | R | E | L | R | R | R | N | I | H | N | A | F | K | L | N | L | F | E | S | A | R | Y | I | K | G | A | W | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | F | V | W | S | T | N | I | A | H | S | I | W | S | A | R | N | S | C | S | T | V | L | V | G | I | V | L | G | P | A | A | A | G | L | F | K | I | A | M | T | F | F | D | A | A | G | T | P | A | G | L | L | G | K | S | F | Y | P | E | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | . | . | 340 | . | . | . | . | . | . | . | . | . | 350 | . | . | . | . | .
Sequence |  | M | R | L | D | P | R | T | T | R | P | W | L | L | G | V | K | S | G | L | L | A | G | G | I | G | I | L | V | A | L | A | V | L | I | V | G | K | P | L | I | S | L | V | F | G | V | K | Y | L | E | A | Y | D | L | I
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 |
| c3mkuA_ |

### PDB 3mku chain A

Region: 4 - 355
Aligned: 347
Modelled: 347
Confidence: 100.0%
Identity: 11%
PDB header:transport protein
Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug
PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter

Phyre2
2 |
| c1mqsB_ |

### PDB 1mqs chain B

Region: 1 - 7
Aligned: 7
Modelled: 7
Confidence: 22.6%
Identity: 86%
PDB header:endocytosis/exocytosis
Chain: B: PDB Molecule:integral membrane protein sed5;
PDBTitle: crystal structure of sly1p in complex with an n-terminal2 peptide of sed5p

Phyre2
3 |
| c3j01A_ |

### PDB 3j01 chain A

Region: 284 - 336
Aligned: 53
Modelled: 53
Confidence: 8.1%
Identity: 6%
PDB header:ribosome/ribosomal protein
Chain: A: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: structure of the ribosome-secye complex in the membrane environment

Phyre2
4 |
| d1jo5a_ |

### PDB 1jo5 chain A

Region: 305 - 339
Aligned: 35
Modelled: 35
Confidence: 7.4%
Identity: 17%
Fold: Light-harvesting complex subunits
Superfamily: Light-harvesting complex subunits
Family: Light-harvesting complex subunits

Phyre2
5 |
| c1kdxB_ |

### PDB 1kdx chain B

Region: 5 - 23
Aligned: 19
Modelled: 19
Confidence: 6.3%
Identity: 11%
PDB header:transcription regulation complex
Chain: B: PDB Molecule:creb;
PDBTitle: kix domain of mouse cbp (creb binding protein) in complex2 with phosphorylated kinase inducible domain (pkid) of rat3 creb (cyclic amp response element binding protein), nmr 174 structures

Phyre2
6 |
| c2vckC_ |

### PDB 2vck chain C

Region: 336 - 352
Aligned: 17
Modelled: 17
Confidence: 6.2%
Identity: 24%
PDB header:oxidoreductase
Chain: C: PDB Molecule:cyanobacterial phycoerythrobilin;
PDBTitle: structure of phycoerythrobilin synthase pebs from the2 cyanophage p-ssm2 in complex with the bound substrate3 biliverdin ixa

Phyre2
7 |
| d1u17a1 |

### PDB 1u17 chain A domain 1

Region: 1 - 13
Aligned: 13
Modelled: 13
Confidence: 6.0%
Identity: 31%
Fold: Lipocalins
Superfamily: Lipocalins
Family: Retinol binding protein-like

Phyre2
8 |
| c2nzzA_ |

### PDB 2nzz chain A

Region: 6 - 16
Aligned: 11
Modelled: 11
Confidence: 6.0%
Identity: 36%
PDB header:membrane protein
Chain: A: PDB Molecule:penetratin conjugated gas (374-394) peptide;
PDBTitle: nmr structure analysis of the penetratin conjugated gas2 (374-394) peptide

Phyre2
9 |
| d2r6gf2 |

### PDB 2r6g chain F domain 2

Region: 5 - 48
Aligned: 44
Modelled: 44
Confidence: 5.9%
Identity: 11%
Fold: MetI-like
Superfamily: MetI-like
Family: MetI-like

Phyre2
10 |
| d1x8qa_ |

### PDB 1x8q chain A

Region: 1 - 13
Aligned: 13
Modelled: 13
Confidence: 5.6%
Identity: 31%
Fold: Lipocalins
Superfamily: Lipocalins
Family: Retinol binding protein-like

Phyre2
11 |
| d1akha_ |

### PDB 1akh chain A

Region: 6 - 16
Aligned: 11
Modelled: 11
Confidence: 5.6%
Identity: 27%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Homeodomain

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3mkuA_ |
|  | 100.0 | 11 | PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter
2 | c1mqsB_ |
|  | 22.6 | 86 | PDB header:endocytosis/exocytosis Chain: B: PDB Molecule:integral membrane protein sed5; PDBTitle: crystal structure of sly1p in complex with an n-terminal2 peptide of sed5p
3 | c3j01A_ |
|  | 8.1 | 6 | PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment
4 | d1jo5a_ |
|  | 7.4 | 17 | Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits
5 | c1kdxB_ |
|  | 6.3 | 11 | PDB header:transcription regulation complex Chain: B: PDB Molecule:creb; PDBTitle: kix domain of mouse cbp (creb binding protein) in complex2 with phosphorylated kinase inducible domain (pkid) of rat3 creb (cyclic amp response element binding protein), nmr 174 structures
6 | c2vckC_ |
|  | 6.2 | 24 | PDB header:oxidoreductase Chain: C: PDB Molecule:cyanobacterial phycoerythrobilin; PDBTitle: structure of phycoerythrobilin synthase pebs from the2 cyanophage p-ssm2 in complex with the bound substrate3 biliverdin ixa
7 | d1u17a1 |
|  | 6.0 | 31 | Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like
8 | c2nzzA_ |
|  | 6.0 | 36 | PDB header:membrane protein Chain: A: PDB Molecule:penetratin conjugated gas (374-394) peptide; PDBTitle: nmr structure analysis of the penetratin conjugated gas2 (374-394) peptide
9 | d2r6gf2 |
|  | 5.9 | 11 | Fold:MetI-like Superfamily:MetI-like Family:MetI-like
10 | d1x8qa_ |
|  | 5.6 | 31 | Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like
11 | d1akha_ |
|  | 5.6 | 27 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain

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
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