Phyre 2 Results for A5A618

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | A5A618
Date | Wed Jan 25 15:20:03 GMT 2012
Unique Job ID | bf2de2b29ceddd02

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3nfiB_
Top template information
PDB header:dna binding protein, transcription Chain: B: PDB Molecule:dna-directed rna polymerase i subunit rpa49; PDBTitle: crystal structure of tandem winged helix domain of rna polymerase i2 subunit a49
Confidence and coverage
Confidence: | 18.7% | Coverage: | 69%
20 residues ( 69% of your sequence) have been modelled with 18.7% 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 |

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Sequence |  | M | S | T | D | L | K | F | S | L | V | T | T | I | I | V | L | G | L | I | V | A | V | G | L | T | A | A | L | H
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 |
| c3nfiB_ |

### PDB 3nfi chain B

Region: 1 - 20
Aligned: 20
Modelled: 20
Confidence: 18.7%
Identity: 5%
PDB header:dna binding protein, transcription
Chain: B: PDB Molecule:dna-directed rna polymerase i subunit rpa49;
PDBTitle: crystal structure of tandem winged helix domain of rna polymerase i2 subunit a49

Phyre2
2 |
| c2l27B_ |

### PDB 2l27 chain B

Region: 1 - 16
Aligned: 16
Modelled: 16
Confidence: 10.8%
Identity: 31%
PDB header:membrane protein, peptide binding protei
Chain: B: PDB Molecule:peptide agonist;
PDBTitle: nmr structure of the ecd1 of crf-r1 in complex with a peptide agonist

Phyre2
3 |
| c1q90G_ |

### PDB 1q90 chain G

Region: 14 - 19
Aligned: 6
Modelled: 6
Confidence: 8.4%
Identity: 83%
PDB header:photosynthesis
Chain: G: PDB Molecule:cytochrome b6f complex subunit petg;
PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii

Phyre2
4 |
| d1q90g_ |

### PDB 1q90 chain G

Region: 14 - 19
Aligned: 6
Modelled: 6
Confidence: 8.4%
Identity: 83%
Fold: Single transmembrane helix
Superfamily: PetG subunit of the cytochrome b6f complex
Family: PetG subunit of the cytochrome b6f complex

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3nfiB_ |
|  | 18.7 | 5 | PDB header:dna binding protein, transcription Chain: B: PDB Molecule:dna-directed rna polymerase i subunit rpa49; PDBTitle: crystal structure of tandem winged helix domain of rna polymerase i2 subunit a49
2 | c2l27B_ |
|  | 10.8 | 31 | PDB header:membrane protein, peptide binding protei Chain: B: PDB Molecule:peptide agonist; PDBTitle: nmr structure of the ecd1 of crf-r1 in complex with a peptide agonist
3 | c1q90G_ |
|  | 8.4 | 83 | PDB header:photosynthesis Chain: G: PDB Molecule:cytochrome b6f complex subunit petg; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii
4 | d1q90g_ |
|  | 8.4 | 83 | Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex

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
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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