Phyre 2 Results for P27375

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Email | l.a.kelley@imperial.ac.uk
Description | P27375
Date | Thu Jan 5 11:43:57 GMT 2012
Unique Job ID | 1f515025f65cfa93

Summary |

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

Model (left) based on template d1kl9a1
Top template information
Fold:SAM domain-like Superfamily:eIF2alpha middle domain-like Family:eIF2alpha middle domain-like
Confidence and coverage
Confidence: | 37.4% | Coverage: | 9%
16 residues ( 9% of your sequence) have been modelled with 37.4% 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 | K | Q | E | V | E | K | W | R | P | F | G | H | P | D | G | D | I | R | D | L | S | F | L | D | A | H | Q | A | V | Y | V | Q | H | H | E | G | K | E | P | L | E | Y | R | F | W | V | T | Y | S | L | H | C | F | T | K | D | Y | E | H
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | T | N | E | E | K | Q | S | L | M | Y | H | A | P | K | E | S | R | P | F | C | Q | H | R | Y | N | L | A | R | T | H | L | K | R | T | I | L | A | L | P | E | S | N | V | I | H | A | G | Y | G | S | Y | A | V | I | E | V | D | L | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | .
Sequence |  | G | G | D | K | A | F | Y | F | V | A | F | R | A | F | R | E | K | K | K | L | R | L | H | V | T | S | A | Y | P | I | S | E | K | Q | K | G | K | S | V | K | F | F | T | I | A | Y | N | L | L | R | N | K | Q | L | P | Q | P | S | K
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 |
| d1kl9a1 |

### PDB 1kl9 chain A domain 1

Region: 81 - 97
Aligned: 16
Modelled: 17
Confidence: 37.4%
Identity: 13%
Fold: SAM domain-like
Superfamily: eIF2alpha middle domain-like
Family: eIF2alpha middle domain-like

Phyre2
2 |
| d1q46a1 |

### PDB 1q46 chain A domain 1

Region: 81 - 101
Aligned: 20
Modelled: 21
Confidence: 27.2%
Identity: 20%
Fold: SAM domain-like
Superfamily: eIF2alpha middle domain-like
Family: eIF2alpha middle domain-like

Phyre2
3 |
| c2vtyA_ |

### PDB 2vty chain A

Region: 84 - 103
Aligned: 20
Modelled: 20
Confidence: 18.8%
Identity: 25%
PDB header:apoptosis
Chain: A: PDB Molecule:protein f1;
PDBTitle: vaccinia virus anti-apoptotic f1l is a novel bcl-2-like2 domain swapped dimer

Phyre2
4 |
| d1u84a_ |

### PDB 1u84 chain A

Region: 1 - 20
Aligned: 19
Modelled: 20
Confidence: 12.7%
Identity: 26%
Fold: YugE-like
Superfamily: YugE-like
Family: YugE-like

Phyre2
5 |
| d1fcda3 |

### PDB 1fcd chain A domain 3

Region: 48 - 55
Aligned: 8
Modelled: 8
Confidence: 9.4%
Identity: 25%
Fold: CO dehydrogenase flavoprotein C-domain-like
Superfamily: FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Family: FAD/NAD-linked reductases, dimerisation (C-terminal) domain

Phyre2
6 |
| c3doaA_ |

### PDB 3doa chain A

Region: 123 - 174
Aligned: 51
Modelled: 51
Confidence: 7.5%
Identity: 14%
PDB header:protein binding
Chain: A: PDB Molecule:fibrinogen binding protein;
PDBTitle: the crystal structure of the fibrinogen binding protein from2 staphylococcus aureus

Phyre2
7 |
| c2q8aA_ |

### PDB 2q8a chain A

Region: 130 - 163
Aligned: 34
Modelled: 34
Confidence: 7.4%
Identity: 12%
PDB header:immune system
Chain: A: PDB Molecule:apical membrane antigen 1;
PDBTitle: structure of the malaria antigen ama1 in complex with a growth-2 inhibitory antibody

Phyre2
8 |
| d1sqwa1 |

### PDB 1sqw chain A domain 1

Region: 43 - 68
Aligned: 26
Modelled: 26
Confidence: 7.0%
Identity: 23%
Fold: PUA domain-like
Superfamily: PUA domain-like
Family: PUA domain

Phyre2
9 |
| d1cz5a1 |

### PDB 1cz5 chain A domain 1

Region: 135 - 151
Aligned: 17
Modelled: 17
Confidence: 6.1%
Identity: 18%
Fold: Double psi beta-barrel
Superfamily: ADC-like
Family: Cdc48 N-terminal domain-like

Phyre2
10 |
| d1mv8a1 |

### PDB 1mv8 chain A domain 1

Region: 49 - 58
Aligned: 10
Modelled: 10
Confidence: 5.9%
Identity: 30%
Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like
Family: UDP-glucose/GDP-mannose dehydrogenase dimerisation domain

Phyre2
11 |
| d1dzfa2 |

### PDB 1dzf chain A domain 2

Region: 82 - 130
Aligned: 49
Modelled: 49
Confidence: 5.7%
Identity: 24%
Fold: RPB5-like RNA polymerase subunit
Superfamily: RPB5-like RNA polymerase subunit
Family: RPB5

Phyre2
12 |
| d1tp6a_ |

### PDB 1tp6 chain A

Region: 12 - 45
Aligned: 31
Modelled: 34
Confidence: 5.6%
Identity: 16%
Fold: Cystatin-like
Superfamily: NTF2-like
Family: PA1314-like

Phyre2
13 |
| d1z67a1 |

### PDB 1z67 chain A domain 1

Region: 86 - 104
Aligned: 18
Modelled: 19
Confidence: 5.6%
Identity: 44%
Fold: YidB-like
Superfamily: YidB-like
Family: YidB-like

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1kl9a1 |
|  | 37.4 | 13 | Fold:SAM domain-like Superfamily:eIF2alpha middle domain-like Family:eIF2alpha middle domain-like
2 | d1q46a1 |
|  | 27.2 | 20 | Fold:SAM domain-like Superfamily:eIF2alpha middle domain-like Family:eIF2alpha middle domain-like
3 | c2vtyA_ |
|  | 18.8 | 25 | PDB header:apoptosis Chain: A: PDB Molecule:protein f1; PDBTitle: vaccinia virus anti-apoptotic f1l is a novel bcl-2-like2 domain swapped dimer
4 | d1u84a_ |
|  | 12.7 | 26 | Fold:YugE-like Superfamily:YugE-like Family:YugE-like
5 | d1fcda3 |
|  | 9.4 | 25 | Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain
6 | c3doaA_ |
|  | 7.5 | 14 | PDB header:protein binding Chain: A: PDB Molecule:fibrinogen binding protein; PDBTitle: the crystal structure of the fibrinogen binding protein from2 staphylococcus aureus
7 | c2q8aA_ |
|  | 7.4 | 12 | PDB header:immune system Chain: A: PDB Molecule:apical membrane antigen 1; PDBTitle: structure of the malaria antigen ama1 in complex with a growth-2 inhibitory antibody
8 | d1sqwa1 |
|  | 7.0 | 23 | Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain
9 | d1cz5a1 |
|  | 6.1 | 18 | Fold:Double psi beta-barrel Superfamily:ADC-like Family:Cdc48 N-terminal domain-like
10 | d1mv8a1 |
|  | 5.9 | 30 | Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:UDP-glucose/GDP-mannose dehydrogenase dimerisation domain
11 | d1dzfa2 |
|  | 5.7 | 24 | Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5
12 | d1tp6a_ |
|  | 5.6 | 16 | Fold:Cystatin-like Superfamily:NTF2-like Family:PA1314-like
13 | d1z67a1 |
|  | 5.6 | 44 | Fold:YidB-like Superfamily:YidB-like Family:YidB-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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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