Phyre 2 Results for P0A6J3

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Email | l.a.kelley@imperial.ac.uk
Description | P0A6J3
Date | Thu Jan 5 11:03:16 GMT 2012
Unique Job ID | 0ec2b147adebba5c

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3zs9D_
Top template information
PDB header:hydrolase/transport protein Chain: D: PDB Molecule:golgi to er traffic protein 2; PDBTitle: s. cerevisiae get3-adp-alf4- complex with a cytosolic get2 fragment
Confidence and coverage
Confidence: | 27.4% | Coverage: | 12%
30 residues ( 12% of your sequence) have been modelled with 27.4% confidence by the single highest scoring template.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | V | S | S | F | T | S | A | P | R | S | G | F | Y | Y | F | A | Q | G | W | K | L | V | S | Q | P | G | I | R | R | F | V | I | L | P | L | L | V | N | I | L | L | M | G | G | A | F | W | W | L | F | T | Q | L | D | V | W | I | P | T
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | L | M | S | Y | V | P | D | W | L | Q | W | L | S | Y | L | L | W | P | L | A | V | I | S | V | L | L | V | F | G | Y | F | F | S | T | I | A | N | W | I | A | A | P | F | N | G | L | L | A | E | Q | L | E | A | R | L | T | G | A | T | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | P | D | T | G | I | F | G | I | M | K | D | V | P | R | I | M | K | R | E | W | Q | K | F | A | W | Y | L | P | R | A | I | V | L | L | I | L | Y | F | I | P | G | I | G | Q | T | V | A | P | V | L | W | F | L | F | S | A | W | M | L | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | I | Q | Y | C | D | Y | P | F | D | N | H | K | V | P | F | K | E | M | R | T | A | L | R | T | R | K | I | T | N | M | Q | F | G | A | L | T | S | L | F | T | M | I | P | L | L | N | L | F | I | M | P | V | A | V | C | G | A | T | A | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | .
Sequence |  | W | V | D | C | Y | R | D | K | H | A | M | W | R
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 |
| c3zs9D_ |

### PDB 3zs9 chain D

Region: 193 - 222
Aligned: 30
Modelled: 30
Confidence: 27.4%
Identity: 27%
PDB header:hydrolase/transport protein
Chain: D: PDB Molecule:golgi to er traffic protein 2;
PDBTitle: s. cerevisiae get3-adp-alf4- complex with a cytosolic get2 fragment

Phyre2
2 |
| c2hg5D_ |

### PDB 2hg5 chain D

Region: 213 - 249
Aligned: 35
Modelled: 37
Confidence: 26.9%
Identity: 20%
PDB header:membrane protein
Chain: D: PDB Molecule:kcsa channel;
PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter

Phyre2
3 |
| c3zs9C_ |

### PDB 3zs9 chain C

Region: 193 - 222
Aligned: 30
Modelled: 30
Confidence: 19.6%
Identity: 27%
PDB header:hydrolase/transport protein
Chain: C: PDB Molecule:golgi to er traffic protein 2;
PDBTitle: s. cerevisiae get3-adp-alf4- complex with a cytosolic get2 fragment

Phyre2
4 |
| d1b4ua_ |

### PDB 1b4u chain A

Region: 185 - 220
Aligned: 36
Modelled: 36
Confidence: 17.9%
Identity: 8%
Fold: LigA subunit of an aromatic-ring-opening dioxygenase LigAB
Superfamily: LigA subunit of an aromatic-ring-opening dioxygenase LigAB
Family: LigA subunit of an aromatic-ring-opening dioxygenase LigAB

Phyre2
5 |
| c2ww9B_ |

### PDB 2ww9 chain B

Region: 191 - 228
Aligned: 38
Modelled: 38
Confidence: 14.3%
Identity: 13%
PDB header:ribosome
Chain: B: PDB Molecule:protein transport protein sss1;
PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome

Phyre2
6 |
| c3sjdE_ |

### PDB 3sjd chain E

Region: 194 - 222
Aligned: 29
Modelled: 29
Confidence: 13.7%
Identity: 28%
PDB header:hydrolase/transport protein
Chain: E: PDB Molecule:golgi to er traffic protein 2;
PDBTitle: crystal structure of s. cerevisiae get3 with bound adp-mg2+ in complex2 with get2 cytosolic domain

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3zs9D_ |
|  | 27.4 | 27 | PDB header:hydrolase/transport protein Chain: D: PDB Molecule:golgi to er traffic protein 2; PDBTitle: s. cerevisiae get3-adp-alf4- complex with a cytosolic get2 fragment
2 | c2hg5D_ |
|  | 26.9 | 20 | PDB header:membrane protein Chain: D: PDB Molecule:kcsa channel; PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter
3 | c3zs9C_ |
|  | 19.6 | 27 | PDB header:hydrolase/transport protein Chain: C: PDB Molecule:golgi to er traffic protein 2; PDBTitle: s. cerevisiae get3-adp-alf4- complex with a cytosolic get2 fragment
4 | d1b4ua_ |
|  | 17.9 | 8 | Fold:LigA subunit of an aromatic-ring-opening dioxygenase LigAB Superfamily:LigA subunit of an aromatic-ring-opening dioxygenase LigAB Family:LigA subunit of an aromatic-ring-opening dioxygenase LigAB
5 | c2ww9B_ |
|  | 14.3 | 13 | PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome
6 | c3sjdE_ |
|  | 13.7 | 28 | PDB header:hydrolase/transport protein Chain: E: PDB Molecule:golgi to er traffic protein 2; PDBTitle: crystal structure of s. cerevisiae get3 with bound adp-mg2+ in complex2 with get2 cytosolic domain

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