Phyre 2 Results for P76180

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Email | l.a.kelley@imperial.ac.uk
Description | P76180
Date | Thu Jan 5 12:20:11 GMT 2012
Unique Job ID | e3ee9b02e1b8ae31

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2k1aA_
Top template information
PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment
Confidence and coverage
Confidence: | 39.0% | Coverage: | 20%
29 residues ( 20% of your sequence) have been modelled with 39.0% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | T | T | T | T | P | Q | R | I | G | G | W | L | L | G | P | L | A | W | L | L | V | A | L | L | S | T | T | L | A | L | L | L | Y | T | A | A | L | S | S | P | Q | T | F | Q | T | L | G | G | Q | A | L | T | T | Q | I | L | W | G | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | F | I | T | A | I | A | L | W | Y | Y | T | L | W | L | T | I | A | F | F | K | R | R | R | C | V | P | K | H | Y | I | I | W | L | L | I | S | V | L | L | A | V | K | A | F | A | F | S | P | V | E | D | G | I | A | V | R | Q | L | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  | ? |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | .
Sequence |  | F | T | L | L | A | T | A | L | I | V | P | Y | F | K | R | S | S | R | V | K | A | T | F | V | N | P
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 |
| c2k1aA_ |

### PDB 2k1a chain A

Region: 56 - 84
Aligned: 29
Modelled: 29
Confidence: 39.0%
Identity: 24%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment

Phyre2
2 |
| c2kncA_ |

### PDB 2knc chain A

Region: 56 - 84
Aligned: 29
Modelled: 29
Confidence: 38.5%
Identity: 24%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2
3 |
| c2bbjB_ |

### PDB 2bbj chain B

Region: 66 - 84
Aligned: 19
Modelled: 19
Confidence: 14.4%
Identity: 16%
PDB header:metal transport/membrane protein
Chain: B: PDB Molecule:divalent cation transport-related protein;
PDBTitle: crystal structure of the cora mg2+ transporter

Phyre2
4 |
| c2jpnA_ |

### PDB 2jpn chain A

Region: 135 - 142
Aligned: 8
Modelled: 8
Confidence: 13.5%
Identity: 50%
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase uvsw;
PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1

Phyre2
5 |
| c2lcyA_ |

### PDB 2lcy chain A

Region: 129 - 133
Aligned: 5
Modelled: 5
Confidence: 13.5%
Identity: 60%
PDB header:viral protein
Chain: A: PDB Molecule:virion spike glycoprotein;
PDBTitle: nmr structure of the complete internal fusion loop from ebolavirus gp22 at ph 5.5

Phyre2
6 |
| d2iuba2 |

### PDB 2iub chain A domain 2

Region: 64 - 84
Aligned: 21
Modelled: 21
Confidence: 12.9%
Identity: 14%
Fold: Transmembrane helix hairpin
Superfamily: Magnesium transport protein CorA, transmembrane region
Family: Magnesium transport protein CorA, transmembrane region

Phyre2
7 |
| c3csyJ_ |

### PDB 3csy chain J

Region: 129 - 133
Aligned: 5
Modelled: 5
Confidence: 8.6%
Identity: 60%
PDB header:immune system/viral protein
Chain: J: PDB Molecule:envelope glycoprotein gp2;
PDBTitle: crystal structure of the trimeric prefusion ebola virus glycoprotein2 in complex with a neutralizing antibody from a human survivor

Phyre2
8 |
| c3s88J_ |

### PDB 3s88 chain J

Region: 129 - 133
Aligned: 5
Modelled: 5
Confidence: 7.9%
Identity: 60%
PDB header:immune system/viral protein
Chain: J: PDB Molecule:envelope glycoprotein;
PDBTitle: crystal structure of sudan ebolavirus glycoprotein (strain gulu) bound2 to 16f6

Phyre2
9 |
| d1wixa_ |

### PDB 1wix chain A

Region: 112 - 144
Aligned: 26
Modelled: 33
Confidence: 6.6%
Identity: 27%
Fold: CH domain-like
Superfamily: Hook domain
Family: Hook domain

Phyre2
10 |
| d3ehbb2 |

### PDB 3ehb chain B domain 2

Region: 51 - 103
Aligned: 53
Modelled: 53
Confidence: 6.0%
Identity: 23%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2k1aA_ |
|  | 39.0 | 24 | PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment
2 | c2kncA_ |
|  | 38.5 | 24 | PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
3 | c2bbjB_ |
|  | 14.4 | 16 | PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter
4 | c2jpnA_ |
|  | 13.5 | 50 | PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent dna helicase uvsw; PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1
5 | c2lcyA_ |
|  | 13.5 | 60 | PDB header:viral protein Chain: A: PDB Molecule:virion spike glycoprotein; PDBTitle: nmr structure of the complete internal fusion loop from ebolavirus gp22 at ph 5.5
6 | d2iuba2 |
|  | 12.9 | 14 | Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region
7 | c3csyJ_ |
|  | 8.6 | 60 | PDB header:immune system/viral protein Chain: J: PDB Molecule:envelope glycoprotein gp2; PDBTitle: crystal structure of the trimeric prefusion ebola virus glycoprotein2 in complex with a neutralizing antibody from a human survivor
8 | c3s88J_ |
|  | 7.9 | 60 | PDB header:immune system/viral protein Chain: J: PDB Molecule:envelope glycoprotein; PDBTitle: crystal structure of sudan ebolavirus glycoprotein (strain gulu) bound2 to 16f6
9 | d1wixa_ |
|  | 6.6 | 27 | Fold:CH domain-like Superfamily:Hook domain Family:Hook domain
10 | d3ehbb2 |
|  | 6.0 | 23 | Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region

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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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