Phyre 2 Results for P0AF98

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Email | l.a.kelley@imperial.ac.uk
Description | P0AF98
Date | Thu Jan 5 11:25:41 GMT 2012
Unique Job ID | a48cec17214f211b

Summary |

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

Model (left) based on template c2kncA_
Top template information
PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
Confidence and coverage
Confidence: | 11.1% | Coverage: | 8%
31 residues ( 8% of your sequence) have been modelled with 11.1% 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.
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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 | I | I | I | R | Y | L | V | R | E | T | L | K | S | Q | L | A | I | L | F | I | L | L | L | I | F | F | C | Q | K | L | V | R | I | L | G | A | A | V | D | G | D | I | P | A | N | L | V | L | S | L | L | G | L | G | V | P | E | M | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | L | I | L | P | L | S | L | F | L | G | L | L | M | T | L | G | K | L | Y | T | E | S | E | I | T | V | M | H | A | C | G | L | S | K | A | V | L | V | K | A | A | M | I | L | A | V | F | T | A | I | V | A | A | V | N | V | M | W | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | G | P | W | S | S | R | H | Q | D | E | V | L | A | E | A | K | A | N | P | G | M | A | A | L | A | Q | G | Q | F | Q | Q | A | T | N | G | S | S | V | L | F | I | E | S | V | D | G | S | D | F | K | D | V | F | L | A | Q | I | R | P | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | G | N | A | R | P | S | V | V | V | A | D | S | G | H | L | T | Q | L | R | D | G | S | Q | V | V | T | L | N | Q | G | T | R | F | E | G | T | A | L | L | R | D | F | R | I | T | D | F | Q | D | Y | Q | A | I | I | G | H | Q | A | V | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | L | D | P | N | D | T | D | Q | M | D | M | R | T | L | W | N | T | D | T | D | R | A | R | A | E | L | N | W | R | I | T | L | V | F | T | V | F | M | M | A | L | M | V | V | P | L | S | V | V | N | P | R | Q | G | R | V | L | S | M | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | . | 330 | . | . | . | . | . | . | . | . | . | 340 | . | . | . | . | . | . | . | . | . | 350 | . | . | . | . | . | . | . | . | . | 360
Sequence |  | P | A | M | L | L | Y | L | L | F | F | L | I | Q | T | S | L | K | S | N | G | G | K | G | K | L | D | P | T | L | W | M | W | T | V | N | L | I | Y | L | A | L | A | I | V | L | N | L | W | D | T | V | P | V | R | R | L | R | A | S | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | .
Sequence |  | S | R | K | G | A | V
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 |
| c2kncA_ |

### PDB 2knc chain A

Region: 332 - 363
Aligned: 31
Modelled: 32
Confidence: 11.1%
Identity: 13%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2
2 |
| c2rdcA_ |

### PDB 2rdc chain A

Region: 2 - 11
Aligned: 10
Modelled: 10
Confidence: 9.1%
Identity: 40%
PDB header:lipid binding protein
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution

Phyre2
3 |
| c2l9uA_ |

### PDB 2l9u chain A

Region: 335 - 354
Aligned: 20
Modelled: 20
Confidence: 7.8%
Identity: 15%
PDB header:membrane protein
Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3;
PDBTitle: spatial structure of dimeric erbb3 transmembrane domain

Phyre2
4 |
| c2voyH_ |

### PDB 2voy chain H

Region: 44 - 83
Aligned: 40
Modelled: 40
Confidence: 7.2%
Identity: 10%
PDB header:hydrolase
Chain: H: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium
PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus

Phyre2
5 |
| d1f5qb1 |

### PDB 1f5q chain B domain 1

Region: 2 - 31
Aligned: 30
Modelled: 30
Confidence: 7.0%
Identity: 3%
Fold: Cyclin-like
Superfamily: Cyclin-like
Family: Cyclin

Phyre2
6 |
| c1mhsA_ |

### PDB 1mhs chain A

Region: 7 - 83
Aligned: 69
Modelled: 77
Confidence: 7.0%
Identity: 14%
PDB header:membrane protein, proton transport
Chain: A: PDB Molecule:plasma membrane atpase;
PDBTitle: model of neurospora crassa proton atpase

Phyre2
7 |
| c2bbjB_ |

### PDB 2bbj chain B

Region: 281 - 350
Aligned: 68
Modelled: 70
Confidence: 6.7%
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
8 |
| c2zxeA_ |

### PDB 2zxe chain A

Region: 8 - 83
Aligned: 68
Modelled: 76
Confidence: 5.8%
Identity: 13%
PDB header:hydrolase/transport protein
Chain: A: PDB Molecule:na, k-atpase alpha subunit;
PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state

Phyre2
9 |
| d1rutx1 |

### PDB 1rut chain X domain 1

Region: 2 - 9
Aligned: 8
Modelled: 8
Confidence: 5.6%
Identity: 38%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
10 |
| d1oeda_ |

### PDB 1oed chain A

Region: 6 - 125
Aligned: 120
Modelled: 120
Confidence: 5.2%
Identity: 8%
Fold: Neurotransmitter-gated ion-channel transmembrane pore
Superfamily: Neurotransmitter-gated ion-channel transmembrane pore
Family: Neurotransmitter-gated ion-channel transmembrane pore

Phyre2
11 |
| c2kr6A_ |

### PDB 2kr6 chain A

Region: 307 - 357
Aligned: 51
Modelled: 51
Confidence: 5.2%
Identity: 20%
PDB header:hydrolase
Chain: A: PDB Molecule:presenilin-1;
PDBTitle: solution structure of presenilin-1 ctf subunit

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2kncA_ |
|  | 11.1 | 13 | PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
2 | c2rdcA_ |
|  | 9.1 | 40 | PDB header:lipid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution
3 | c2l9uA_ |
|  | 7.8 | 15 | PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain
4 | c2voyH_ |
|  | 7.2 | 10 | PDB header:hydrolase Chain: H: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus
5 | d1f5qb1 |
|  | 7.0 | 3 | Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin
6 | c1mhsA_ |
|  | 7.0 | 14 | PDB header:membrane protein, proton transport Chain: A: PDB Molecule:plasma membrane atpase; PDBTitle: model of neurospora crassa proton atpase
7 | c2bbjB_ |
|  | 6.7 | 16 | PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter
8 | c2zxeA_ |
|  | 5.8 | 13 | PDB header:hydrolase/transport protein Chain: A: PDB Molecule:na, k-atpase alpha subunit; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state
9 | d1rutx1 |
|  | 5.6 | 38 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
10 | d1oeda_ |
|  | 5.2 | 8 | Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore
11 | c2kr6A_ |
|  | 5.2 | 20 | PDB header:hydrolase Chain: A: PDB Molecule:presenilin-1; PDBTitle: solution structure of presenilin-1 ctf subunit

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