Phyre 2 Results for P08339

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P08339
Date | Thu Jan 5 11:01:11 GMT 2012
Unique Job ID | d8d1658deff2e7d6

Summary |

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

Model (left) based on template c1nvpC_
Top template information
PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia beta chain; PDBTitle: human tfiia/tbp/dna complex
Confidence and coverage
Confidence: | 43.2% | Coverage: | 10%
9 residues ( 10% of your sequence) have been modelled with 43.2% 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.
Please note: You must be registered and logged in to use Phyrealarm.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | H | M | V | T | Y | P | C | L | T | S | R | R | F | Q | L | A | L | I | H | R | R | V | V | D | K | R | T | S | M | H | S | R | T | A | S | E | S | T | G | A | R | I | H | R | P | W | C | A | R | H | Q | V | R | P | A | W | R | C | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | .
Sequence |  | Y | D | K | L | H | R | V | P | F | R | S | P | E | L | R | L | D | S | G | P | G | Y | T | T | G | S | Y | R | Y
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 |
| c1nvpC_ |

### PDB 1nvp chain C

Region: 59 - 67
Aligned: 9
Modelled: 9
Confidence: 43.2%
Identity: 78%
PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia beta chain;
PDBTitle: human tfiia/tbp/dna complex

Phyre2
2 |
| d1nvpc_ |

### PDB 1nvp chain C

Region: 59 - 67
Aligned: 9
Modelled: 9
Confidence: 43.2%
Identity: 78%
Fold: Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
Family: Transcription factor IIA (TFIIA), beta-barrel domain

Phyre2
3 |
| d1nh2c_ |

### PDB 1nh2 chain C

Region: 59 - 67
Aligned: 9
Modelled: 9
Confidence: 42.0%
Identity: 56%
Fold: Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
Family: Transcription factor IIA (TFIIA), beta-barrel domain

Phyre2
4 |
| c1nh2C_ |

### PDB 1nh2 chain C

Region: 59 - 67
Aligned: 9
Modelled: 9
Confidence: 42.0%
Identity: 56%
PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia large chain;
PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex

Phyre2
5 |
| d1ytfc_ |

### PDB 1ytf chain C

Region: 59 - 67
Aligned: 9
Modelled: 9
Confidence: 40.1%
Identity: 56%
Fold: Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
Family: Transcription factor IIA (TFIIA), beta-barrel domain

Phyre2
6 |
| c3eatX_ |

### PDB 3eat chain X

Region: 23 - 77
Aligned: 41
Modelled: 55
Confidence: 34.2%
Identity: 27%
PDB header:oxidoreductase
Chain: X: PDB Molecule:pyoverdine biosynthesis protein pvcb;
PDBTitle: crystal structure of the pvcb (pa2255) protein from2 pseudomonas aeruginosa

Phyre2
7 |
| c1rm1C_ |

### PDB 1rm1 chain C

Region: 59 - 67
Aligned: 9
Modelled: 9
Confidence: 28.7%
Identity: 56%
PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia large chain;
PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex

Phyre2
8 |
| d2vy4a1 |

### PDB 2vy4 chain A domain 1

Region: 59 - 73
Aligned: 15
Modelled: 15
Confidence: 24.1%
Identity: 40%
Fold: beta-beta-alpha zinc fingers
Superfamily: beta-beta-alpha zinc fingers
Family: CHHC finger

Phyre2
9 |
| c3pvjB_ |

### PDB 3pvj chain B

Region: 23 - 49
Aligned: 27
Modelled: 27
Confidence: 9.0%
Identity: 22%
PDB header:oxidoreductase
Chain: B: PDB Molecule:alpha-ketoglutarate-dependent taurine dioxygenase;
PDBTitle: crystal structure of the fe(ii)/alpha-ketoglutarate dependent taurine2 dioxygenase from pseudomonas putida kt2440

Phyre2
10 |
| d3c96a2 |

### PDB 3c96 chain A domain 2

Region: 2 - 8
Aligned: 7
Modelled: 7
Confidence: 8.0%
Identity: 43%
Fold: FAD-linked reductases, C-terminal domain
Superfamily: FAD-linked reductases, C-terminal domain
Family: PHBH-like

Phyre2
11 |
| d1x3ha2 |

### PDB 1x3h chain A domain 2

Region: 45 - 51
Aligned: 7
Modelled: 7
Confidence: 7.9%
Identity: 57%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
12 |
| d1m06f_ |

### PDB 1m06 chain F

Region: 60 - 85
Aligned: 20
Modelled: 26
Confidence: 7.0%
Identity: 55%
Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily: ssDNA viruses
Family: Microviridae-like VP

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1nvpC_ |
|  | 43.2 | 78 | PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia beta chain; PDBTitle: human tfiia/tbp/dna complex
2 | d1nvpc_ |
|  | 43.2 | 78 | Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain
3 | d1nh2c_ |
|  | 42.0 | 56 | Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain
4 | c1nh2C_ |
|  | 42.0 | 56 | PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia large chain; PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex
5 | d1ytfc_ |
|  | 40.1 | 56 | Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain
6 | c3eatX_ |
|  | 34.2 | 27 | PDB header:oxidoreductase Chain: X: PDB Molecule:pyoverdine biosynthesis protein pvcb; PDBTitle: crystal structure of the pvcb (pa2255) protein from2 pseudomonas aeruginosa
7 | c1rm1C_ |
|  | 28.7 | 56 | PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia large chain; PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex
8 | d2vy4a1 |
|  | 24.1 | 40 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:CHHC finger
9 | c3pvjB_ |
|  | 9.0 | 22 | PDB header:oxidoreductase Chain: B: PDB Molecule:alpha-ketoglutarate-dependent taurine dioxygenase; PDBTitle: crystal structure of the fe(ii)/alpha-ketoglutarate dependent taurine2 dioxygenase from pseudomonas putida kt2440
10 | d3c96a2 |
|  | 8.0 | 43 | Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:PHBH-like
11 | d1x3ha2 |
|  | 7.9 | 57 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
12 | d1m06f_ |
|  | 7.0 | 55 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Microviridae-like VP

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