Phyre 2 Results for P77858

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Email | l.a.kelley@imperial.ac.uk
Description | P77858
Date | Wed Jan 25 15:21:12 GMT 2012
Unique Job ID | 6a2526dbf698df17

Summary |

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

Model (left) based on template c3rkoL_
Top template information
PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution
Confidence and coverage
Confidence: | 91.3% | Coverage: | 40%
127 residues ( 40% of your sequence) have been modelled with 91.3% 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 | R | Q | T | L | C | D | G | Y | L | V | I | F | A | L | A | Q | A | V | I | L | L | M | L | T | P | L | F | T | G | I | S | R | Q | I | R | A | R | M | H | S | R | R | G | P | G | I | W | Q | D | Y | R | D | I | H | K | L | F | K | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | E | V | A | P | T | S | S | G | L | M | F | R | L | M | P | W | V | L | I | S | S | M | L | V | L | A | M | A | L | P | L | F | I | T | V | S | P | F | A | G | G | G | D | L | I | T | L | I | Y | L | L | A | L | F | R | F | F | F | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | L | S | G | L | D | T | G | S | P | F | A | G | V | G | A | S | R | E | L | T | L | G | I | L | V | E | P | M | L | I | L | S | L | L | V | L | A | L | I | A | G | S | T | H | I | E | M | I | S | N | T | L | A | M | G | W | N | S | P | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  | ? |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | T | T | V | L | A | L | L | A | C | G | F | A | C | F | I | E | M | G | K | I | P | F | D | V | A | E | A | E | Q | E | L | Q | E | G | P | L | T | E | Y | S | G | A | G | L | A | L | A | K | W | G | L | G | L | K | Q | V | V | M | A | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | L | F | V | A | L | F | L | P | F | G | R | A | Q | E | L | S | L | A | C | L | L | T | S | L | V | V | T | L | L | K | V | L | L | I | F | V | L | A | S | I | A | E | N | T | L | A | R | G | R | F | L | L | I | H | H | V | T | W | L | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | .
Sequence |  | F | S | L | A | A | L | A | W | V | F | W | L | T | G | 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 |
| c3rkoL_ |

### PDB 3rko chain L

Region: 84 - 210
Aligned: 127
Modelled: 127
Confidence: 91.3%
Identity: 13%
PDB header:oxidoreductase
Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l;
PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution

Phyre2
2 |
| c1q2iA_ |

### PDB 1q2i chain A

Region: 45 - 60
Aligned: 16
Modelled: 16
Confidence: 39.9%
Identity: 38%
PDB header:antitumor protein
Chain: A: PDB Molecule:pnc27;
PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells

Phyre2
3 |
| c2jpmA_ |

### PDB 2jpm chain A

Region: 46 - 63
Aligned: 18
Modelled: 18
Confidence: 22.9%
Identity: 11%
PDB header:antimicrobial protein
Chain: A: PDB Molecule:bacteriocin lactococcin-g subunit beta;
PDBTitle: lactococcin g-b in tfe

Phyre2
4 |
| d1lbqa_ |

### PDB 1lbq chain A

Region: 40 - 61
Aligned: 22
Modelled: 22
Confidence: 17.9%
Identity: 18%
Fold: Chelatase-like
Superfamily: Chelatase
Family: Ferrochelatase

Phyre2
5 |
| d1xn8a_ |

### PDB 1xn8 chain A

Region: 202 - 232
Aligned: 31
Modelled: 31
Confidence: 14.2%
Identity: 26%
Fold: Hypothetical protein YqbG
Superfamily: Hypothetical protein YqbG
Family: Hypothetical protein YqbG

Phyre2
6 |
| d1ufra_ |

### PDB 1ufr chain A

Region: 202 - 221
Aligned: 20
Modelled: 20
Confidence: 9.8%
Identity: 20%
Fold: PRTase-like
Superfamily: PRTase-like
Family: Phosphoribosyltransferases (PRTases)

Phyre2
7 |
| c3rkoM_ |

### PDB 3rko chain M

Region: 79 - 280
Aligned: 194
Modelled: 195
Confidence: 9.2%
Identity: 16%
PDB header:oxidoreductase
Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m;
PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution

Phyre2
8 |
| c2k8fB_ |

### PDB 2k8f chain B

Region: 43 - 65
Aligned: 23
Modelled: 23
Confidence: 6.8%
Identity: 26%
PDB header:transferase/transcription
Chain: B: PDB Molecule:cellular tumor antigen p53;
PDBTitle: structural basis for the regulation of p53 function by p300

Phyre2
9 |
| c2vxsB_ |

### PDB 2vxs chain B

Region: 198 - 208
Aligned: 11
Modelled: 10
Confidence: 6.7%
Identity: 27%
PDB header:cytokine
Chain: B: PDB Molecule:interleukin-17a;
PDBTitle: structure of il-17a in complex with a potent, fully human2 neutralising antibody

Phyre2
10 |
| c2rmrA_ |

### PDB 2rmr chain A

Region: 33 - 63
Aligned: 29
Modelled: 31
Confidence: 5.7%
Identity: 34%
PDB header:transcription
Chain: A: PDB Molecule:paired amphipathic helix protein sin3a;
PDBTitle: solution structure of msin3a pah1 domain

Phyre2
11 |
| d2hrca1 |

### PDB 2hrc chain A domain 1

Region: 40 - 61
Aligned: 22
Modelled: 22
Confidence: 5.7%
Identity: 18%
Fold: Chelatase-like
Superfamily: Chelatase
Family: Ferrochelatase

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3rkoL_ |
|  | 91.3 | 13 | PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution
2 | c1q2iA_ |
|  | 39.9 | 38 | PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells
3 | c2jpmA_ |
|  | 22.9 | 11 | PDB header:antimicrobial protein Chain: A: PDB Molecule:bacteriocin lactococcin-g subunit beta; PDBTitle: lactococcin g-b in tfe
4 | d1lbqa_ |
|  | 17.9 | 18 | Fold:Chelatase-like Superfamily:Chelatase Family:Ferrochelatase
5 | d1xn8a_ |
|  | 14.2 | 26 | Fold:Hypothetical protein YqbG Superfamily:Hypothetical protein YqbG Family:Hypothetical protein YqbG
6 | d1ufra_ |
|  | 9.8 | 20 | Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases)
7 | c3rkoM_ |
|  | 9.2 | 16 | PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution
8 | c2k8fB_ |
|  | 6.8 | 26 | PDB header:transferase/transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structural basis for the regulation of p53 function by p300
9 | c2vxsB_ |
|  | 6.7 | 27 | PDB header:cytokine Chain: B: PDB Molecule:interleukin-17a; PDBTitle: structure of il-17a in complex with a potent, fully human2 neutralising antibody
10 | c2rmrA_ |
|  | 5.7 | 34 | PDB header:transcription Chain: A: PDB Molecule:paired amphipathic helix protein sin3a; PDBTitle: solution structure of msin3a pah1 domain
11 | d2hrca1 |
|  | 5.7 | 18 | Fold:Chelatase-like Superfamily:Chelatase Family:Ferrochelatase

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