Phyre 2 Results for P76078

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Email | l.a.kelley@imperial.ac.uk
Description | P76078
Date | Thu Jan 5 12:18:17 GMT 2012
Unique Job ID | 3c9b8db3a6d38746

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3egrB_
Top template information
PDB header:oxidoreductase Chain: B: PDB Molecule:phenylacetate-coa oxygenase subunit paab; PDBTitle: crystal structure of a phenylacetate-coa oxygenase subunit paab2 (reut_a2307) from ralstonia eutropha jmp134 at 2.65 a resolution
Confidence and coverage
Confidence: | 100.0% | Coverage: | 65%
62 residues ( 65% of your sequence) have been modelled with 100.0% 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 | S | N | V | Y | W | P | L | Y | E | V | F | V | R | G | K | Q | G | L | S | H | R | H | V | G | S | L | H | A | A | D | E | R | M | A | L | E | N | A | R | D | A | Y | T | R | R | S | E | G | C | S | I | W | V | V | K | A | S | E | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | .
Sequence |  | V | A | S | Q | P | E | E | R | G | E | F | F | D | P | A | E | S | K | V | Y | R | H | P | T | F | Y | T | I | P | D | G | I | E | H | M
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 |
| c3egrB_ |

### PDB 3egr chain B

Region: 4 - 65
Aligned: 62
Modelled: 62
Confidence: 100.0%
Identity: 65%
PDB header:oxidoreductase
Chain: B: PDB Molecule:phenylacetate-coa oxygenase subunit paab;
PDBTitle: crystal structure of a phenylacetate-coa oxygenase subunit paab2 (reut_a2307) from ralstonia eutropha jmp134 at 2.65 a resolution

Phyre2
2 |
| d1na6a1 |

### PDB 1na6 chain A domain 1

Region: 49 - 59
Aligned: 11
Modelled: 11
Confidence: 14.2%
Identity: 27%
Fold: DNA-binding pseudobarrel domain
Superfamily: DNA-binding pseudobarrel domain
Family: Type II restriction endonuclease effector domain

Phyre2
3 |
| d2fgca2 |

### PDB 2fgc chain A domain 2

Region: 22 - 52
Aligned: 29
Modelled: 31
Confidence: 12.5%
Identity: 21%
Fold: Ferredoxin-like
Superfamily: ACT-like
Family: IlvH-like

Phyre2
4 |
| d2f1fa1 |

### PDB 2f1f chain A domain 1

Region: 22 - 52
Aligned: 29
Modelled: 31
Confidence: 10.2%
Identity: 28%
Fold: Ferredoxin-like
Superfamily: ACT-like
Family: IlvH-like

Phyre2
5 |
| c2j6aA_ |

### PDB 2j6a chain A

Region: 83 - 95
Aligned: 13
Modelled: 13
Confidence: 9.7%
Identity: 31%
PDB header:transferase
Chain: A: PDB Molecule:protein trm112;
PDBTitle: crystal structure of s. cerevisiae ynr046w, a zinc finger2 protein from the erf1 methyltransferase complex.

Phyre2
6 |
| d2pc6a2 |

### PDB 2pc6 chain A domain 2

Region: 21 - 52
Aligned: 30
Modelled: 31
Confidence: 9.5%
Identity: 33%
Fold: Ferredoxin-like
Superfamily: ACT-like
Family: IlvH-like

Phyre2
7 |
| d1a0ia1 |

### PDB 1a0i chain A domain 1

Region: 68 - 85
Aligned: 18
Modelled: 18
Confidence: 7.9%
Identity: 22%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: DNA ligase/mRNA capping enzyme postcatalytic domain

Phyre2
8 |
| c2f1fA_ |

### PDB 2f1f chain A

Region: 22 - 52
Aligned: 29
Modelled: 31
Confidence: 6.8%
Identity: 28%
PDB header:transferase
Chain: A: PDB Molecule:acetolactate synthase isozyme iii small subunit;
PDBTitle: crystal structure of the regulatory subunit of2 acetohydroxyacid synthase isozyme iii from e. coli

Phyre2
9 |
| d1wv8a1 |

### PDB 1wv8 chain A domain 1

Region: 44 - 60
Aligned: 16
Modelled: 17
Confidence: 6.5%
Identity: 19%
Fold: TTHA1013/TTHA0281-like
Superfamily: TTHA1013/TTHA0281-like
Family: TTHA1013-like

Phyre2
10 |
| c2pc6C_ |

### PDB 2pc6 chain C

Region: 22 - 52
Aligned: 29
Modelled: 31
Confidence: 6.2%
Identity: 34%
PDB header:lyase
Chain: C: PDB Molecule:probable acetolactate synthase isozyme iii (small subunit);
PDBTitle: crystal structure of putative acetolactate synthase- small subunit2 from nitrosomonas europaea

Phyre2
11 |
| d2gu3a1 |

### PDB 2gu3 chain A domain 1

Region: 7 - 18
Aligned: 12
Modelled: 12
Confidence: 6.0%
Identity: 42%
Fold: Cystatin-like
Superfamily: Cystatin/monellin
Family: PepSY-like

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3egrB_ |
|  | 100.0 | 65 | PDB header:oxidoreductase Chain: B: PDB Molecule:phenylacetate-coa oxygenase subunit paab; PDBTitle: crystal structure of a phenylacetate-coa oxygenase subunit paab2 (reut_a2307) from ralstonia eutropha jmp134 at 2.65 a resolution
2 | d1na6a1 |
|  | 14.2 | 27 | Fold:DNA-binding pseudobarrel domain Superfamily:DNA-binding pseudobarrel domain Family:Type II restriction endonuclease effector domain
3 | d2fgca2 |
|  | 12.5 | 21 | Fold:Ferredoxin-like Superfamily:ACT-like Family:IlvH-like
4 | d2f1fa1 |
|  | 10.2 | 28 | Fold:Ferredoxin-like Superfamily:ACT-like Family:IlvH-like
5 | c2j6aA_ |
|  | 9.7 | 31 | PDB header:transferase Chain: A: PDB Molecule:protein trm112; PDBTitle: crystal structure of s. cerevisiae ynr046w, a zinc finger2 protein from the erf1 methyltransferase complex.
6 | d2pc6a2 |
|  | 9.5 | 33 | Fold:Ferredoxin-like Superfamily:ACT-like Family:IlvH-like
7 | d1a0ia1 |
|  | 7.9 | 22 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA ligase/mRNA capping enzyme postcatalytic domain
8 | c2f1fA_ |
|  | 6.8 | 28 | PDB header:transferase Chain: A: PDB Molecule:acetolactate synthase isozyme iii small subunit; PDBTitle: crystal structure of the regulatory subunit of2 acetohydroxyacid synthase isozyme iii from e. coli
9 | d1wv8a1 |
|  | 6.5 | 19 | Fold:TTHA1013/TTHA0281-like Superfamily:TTHA1013/TTHA0281-like Family:TTHA1013-like
10 | c2pc6C_ |
|  | 6.2 | 34 | PDB header:lyase Chain: C: PDB Molecule:probable acetolactate synthase isozyme iii (small subunit); PDBTitle: crystal structure of putative acetolactate synthase- small subunit2 from nitrosomonas europaea
11 | d2gu3a1 |
|  | 6.0 | 42 | Fold:Cystatin-like Superfamily:Cystatin/monellin Family:PepSY-like

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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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