Phyre 2 Results for P64439

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P64439
Date | Thu Jan 5 12:08:20 GMT 2012
Unique Job ID | 91d1f05f354cc936

Summary |

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

Model (left) based on template c2zxxA_
Top template information
PDB header:cell cycle/replication Chain: A: PDB Molecule:geminin; PDBTitle: crystal structure of cdt1/geminin complex
Confidence and coverage
Confidence: | 31.0% | Coverage: | 9%
11 residues ( 9% of your sequence) have been modelled with 31.0% 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.
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 | K | H | K | Q | R | W | A | G | A | I | C | C | F | V | L | F | I | V | V | C | L | F | L | A | T | H | M | K | G | A | F | R | A | A | G | H | P | E | I | G | L | L | F | F | I | L | P | G | A | V | A | S | F | F | S | Q | R | R | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | V | L | K | P | L | F | G | A | M | L | A | A | P | C | S | M | L | I | M | R | L | F | F | S | P | T | R | S | F | W | Q | E | L | A | W | L | L | S | A | V | F | W | C | A | L | G | A | L | C | F | L | F | I | S | S | L | F | K | P | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | .
Sequence |  | H | R | K | N | Q
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 |
| c2zxxA_ |

### PDB 2zxx chain A

Region: 84 - 94
Aligned: 11
Modelled: 11
Confidence: 31.0%
Identity: 36%
PDB header:cell cycle/replication
Chain: A: PDB Molecule:geminin;
PDBTitle: crystal structure of cdt1/geminin complex

Phyre2
2 |
| d1i5pa3 |

### PDB 1i5p chain A domain 3

Region: 49 - 93
Aligned: 39
Modelled: 45
Confidence: 22.3%
Identity: 21%
Fold: Toxins' membrane translocation domains
Superfamily: delta-Endotoxin (insectocide), N-terminal domain
Family: delta-Endotoxin (insectocide), N-terminal domain

Phyre2
3 |
| c2wvrB_ |

### PDB 2wvr chain B

Region: 84 - 94
Aligned: 11
Modelled: 11
Confidence: 19.2%
Identity: 36%
PDB header:replication
Chain: B: PDB Molecule:geminin;
PDBTitle: human cdt1:geminin complex

Phyre2
4 |
| d1fo8a_ |

### PDB 1fo8 chain A

Region: 87 - 125
Aligned: 29
Modelled: 39
Confidence: 10.0%
Identity: 28%
Fold: Nucleotide-diphospho-sugar transferases
Superfamily: Nucleotide-diphospho-sugar transferases
Family: N-acetylglucosaminyltransferase I

Phyre2
5 |
| c1iijA_ |

### PDB 1iij chain A

Region: 41 - 60
Aligned: 20
Modelled: 20
Confidence: 9.8%
Identity: 30%
PDB header:signaling protein
Chain: A: PDB Molecule:erbb-2 receptor protein-tyrosine kinase;
PDBTitle: solution structure of the neu/erbb-2 membrane spanning2 segment

Phyre2
6 |
| c1z65A_ |

### PDB 1z65 chain A

Region: 7 - 18
Aligned: 12
Modelled: 12
Confidence: 9.6%
Identity: 42%
PDB header:unknown function
Chain: A: PDB Molecule:prion-like protein doppel;
PDBTitle: mouse doppel 1-30 peptide

Phyre2
7 |
| d1x4la2 |

### PDB 1x4l chain A domain 2

Region: 53 - 68
Aligned: 16
Modelled: 16
Confidence: 7.6%
Identity: 31%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
8 |
| d1ffgb_ |

### PDB 1ffg chain B

Region: 9 - 15
Aligned: 7
Modelled: 7
Confidence: 7.3%
Identity: 57%
Fold: Ferredoxin-like
Superfamily: CheY-binding domain of CheA
Family: CheY-binding domain of CheA

Phyre2
9 |
| d1eysh2 |

### PDB 1eys chain H domain 2

Region: 110 - 124
Aligned: 15
Modelled: 15
Confidence: 7.2%
Identity: 20%
Fold: Single transmembrane helix
Superfamily: Photosystem II reaction centre subunit H, transmembrane region
Family: Photosystem II reaction centre subunit H, transmembrane region

Phyre2
10 |
| c1a0oH_ |

### PDB 1a0o chain H

Region: 9 - 15
Aligned: 7
Modelled: 7
Confidence: 7.2%
Identity: 57%
PDB header:chemotaxis
Chain: H: PDB Molecule:chea;
PDBTitle: chey-binding domain of chea in complex with chey

Phyre2
11 |
| d1q3ja_ |

### PDB 1q3j chain A

Region: 48 - 58
Aligned: 11
Modelled: 11
Confidence: 5.8%
Identity: 36%
Fold: Knottins (small inhibitors, toxins, lectins)
Superfamily: Gurmarin-like
Family: Antifungal peptide

Phyre2
12 |
| c1bhbA_ |

### PDB 1bhb chain A

Region: 38 - 50
Aligned: 13
Modelled: 13
Confidence: 5.8%
Identity: 31%
PDB header:photoreceptor
Chain: A: PDB Molecule:bacteriorhodopsin;
PDBTitle: three-dimensional structure of (1-71) bacterioopsin2 solubilized in methanol-chloroform and sds micelles3 determined by 15n-1h heteronuclear nmr spectroscopy

Phyre2
13 |
| c3t7hB_ |

### PDB 3t7h chain B

Region: 86 - 94
Aligned: 9
Modelled: 9
Confidence: 5.7%
Identity: 56%
PDB header:ligase
Chain: B: PDB Molecule:ubiquitin-like modifier-activating enzyme atg7;
PDBTitle: atg8 transfer from atg7 to atg3: a distinctive e1-e2 architecture and2 mechanism in the autophagy pathway

Phyre2
14 |
| c3hlsE_ |

### PDB 3hls chain E

Region: 42 - 52
Aligned: 11
Modelled: 11
Confidence: 5.2%
Identity: 55%
PDB header:signaling protein
Chain: E: PDB Molecule:guanylate cyclase soluble subunit beta-1;
PDBTitle: crystal structure of the signaling helix coiled-coil doimain2 of the beta-1 subunit of the soluble guanylyl cyclase

Phyre2
15 |
| c3n0aA_ |

### PDB 3n0a chain A

Region: 1 - 18
Aligned: 18
Modelled: 18
Confidence: 5.2%
Identity: 6%
PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase auxilin;
PDBTitle: crystal structure of auxilin (40-400)

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2zxxA_ |
|  | 31.0 | 36 | PDB header:cell cycle/replication Chain: A: PDB Molecule:geminin; PDBTitle: crystal structure of cdt1/geminin complex
2 | d1i5pa3 |
|  | 22.3 | 21 | Fold:Toxins' membrane translocation domains Superfamily:delta-Endotoxin (insectocide), N-terminal domain Family:delta-Endotoxin (insectocide), N-terminal domain
3 | c2wvrB_ |
|  | 19.2 | 36 | PDB header:replication Chain: B: PDB Molecule:geminin; PDBTitle: human cdt1:geminin complex
4 | d1fo8a_ |
|  | 10.0 | 28 | Fold:Nucleotide-diphospho-sugar transferases Superfamily:Nucleotide-diphospho-sugar transferases Family:N-acetylglucosaminyltransferase I
5 | c1iijA_ |
|  | 9.8 | 30 | PDB header:signaling protein Chain: A: PDB Molecule:erbb-2 receptor protein-tyrosine kinase; PDBTitle: solution structure of the neu/erbb-2 membrane spanning2 segment
6 | c1z65A_ |
|  | 9.6 | 42 | PDB header:unknown function Chain: A: PDB Molecule:prion-like protein doppel; PDBTitle: mouse doppel 1-30 peptide
7 | d1x4la2 |
|  | 7.6 | 31 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
8 | d1ffgb_ |
|  | 7.3 | 57 | Fold:Ferredoxin-like Superfamily:CheY-binding domain of CheA Family:CheY-binding domain of CheA
9 | d1eysh2 |
|  | 7.2 | 20 | Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region
10 | c1a0oH_ |
|  | 7.2 | 57 | PDB header:chemotaxis Chain: H: PDB Molecule:chea; PDBTitle: chey-binding domain of chea in complex with chey
11 | d1q3ja_ |
|  | 5.8 | 36 | Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Gurmarin-like Family:Antifungal peptide
12 | c1bhbA_ |
|  | 5.8 | 31 | PDB header:photoreceptor Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: three-dimensional structure of (1-71) bacterioopsin2 solubilized in methanol-chloroform and sds micelles3 determined by 15n-1h heteronuclear nmr spectroscopy
13 | c3t7hB_ |
|  | 5.7 | 56 | PDB header:ligase Chain: B: PDB Molecule:ubiquitin-like modifier-activating enzyme atg7; PDBTitle: atg8 transfer from atg7 to atg3: a distinctive e1-e2 architecture and2 mechanism in the autophagy pathway
14 | c3hlsE_ |
|  | 5.2 | 55 | PDB header:signaling protein Chain: E: PDB Molecule:guanylate cyclase soluble subunit beta-1; PDBTitle: crystal structure of the signaling helix coiled-coil doimain2 of the beta-1 subunit of the soluble guanylyl cyclase
15 | c3n0aA_ |
|  | 5.2 | 6 | PDB header:hydrolase Chain: A: PDB Molecule:tyrosine-protein phosphatase auxilin; PDBTitle: crystal structure of auxilin (40-400)

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