Phyre 2 Results for P0A8J2

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Email | l.a.kelley@imperial.ac.uk
Description | P0A8J2
Date | Thu Jan 5 11:07:58 GMT 2012
Unique Job ID | 84020cea99e85bf1

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3bjqA_
Top template information
PDB header:viral protein Chain: A: PDB Molecule:phage-related protein; PDBTitle: crystal structure of a phage-related protein (bb3626) from bordetella2 bronchiseptica rb50 at 2.05 a resolution
Confidence and coverage
Confidence: | 25.0% | Coverage: | 20%
35 residues ( 20% of your sequence) have been modelled with 25.0% 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 | S | S | R | V | L | T | P | D | V | V | G | I | D | A | L | V | H | D | H | Q | T | V | L | A | K | A | E | G | G | V | V | A | V | F | A | N | N | A | P | A | F | Y | A | V | T | P | A | R | L | A | E | L | L | A | L | E | E | K | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | A | R | P | G | S | D | V | A | L | D | D | Q | L | Y | Q | E | P | Q | A | A | P | V | A | V | P | M | G | K | F | A | M | Y | P | D | W | Q | P | D | A | D | F | I | R | L | A | A | L | W | G | V | A | L | R | E | P | V | T | T | E | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | .
Sequence |  | L | A | S | F | I | A | Y | W | Q | A | E | G | K | V | F | H | H | V | Q | W | Q | Q | K | L | A | R | S | L | Q | I | G | R | A | S | N | G | G | L | P | K | R | D | V | N | T | V | S | E | P | D | S | Q | I | P | P | G | F | R | G
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 |
| c3bjqA_ |

### PDB 3bjq chain A

Region: 10 - 58
Aligned: 35
Modelled: 48
Confidence: 25.0%
Identity: 23%
PDB header:viral protein
Chain: A: PDB Molecule:phage-related protein;
PDBTitle: crystal structure of a phage-related protein (bb3626) from bordetella2 bronchiseptica rb50 at 2.05 a resolution

Phyre2
2 |
| c2e52A_ |

### PDB 2e52 chain A

Region: 123 - 160
Aligned: 38
Modelled: 38
Confidence: 20.4%
Identity: 26%
PDB header:hydrolase/dna
Chain: A: PDB Molecule:type ii restriction enzyme hindiii;
PDBTitle: crystal structural analysis of hindiii restriction endonuclease in2 complex with cognate dna at 2.0 angstrom resolution

Phyre2
3 |
| d1m9za_ |

### PDB 1m9z chain A

Region: 9 - 25
Aligned: 17
Modelled: 17
Confidence: 18.2%
Identity: 12%
Fold: Snake toxin-like
Superfamily: Snake toxin-like
Family: Extracellular domain of cell surface receptors

Phyre2
4 |
| d1ks6a_ |

### PDB 1ks6 chain A

Region: 9 - 25
Aligned: 17
Modelled: 17
Confidence: 18.0%
Identity: 29%
Fold: Snake toxin-like
Superfamily: Snake toxin-like
Family: Extracellular domain of cell surface receptors

Phyre2
5 |
| d2pjyb1 |

### PDB 2pjy chain B domain 1

Region: 9 - 25
Aligned: 17
Modelled: 17
Confidence: 17.7%
Identity: 12%
Fold: Snake toxin-like
Superfamily: Snake toxin-like
Family: Extracellular domain of cell surface receptors

Phyre2
6 |
| d1ploa_ |

### PDB 1plo chain A

Region: 9 - 25
Aligned: 17
Modelled: 17
Confidence: 16.7%
Identity: 12%
Fold: Snake toxin-like
Superfamily: Snake toxin-like
Family: Extracellular domain of cell surface receptors

Phyre2
7 |
| c2kgmA_ |

### PDB 2kgm chain A

Region: 129 - 156
Aligned: 22
Modelled: 28
Confidence: 14.9%
Identity: 41%
PDB header:signaling protein
Chain: A: PDB Molecule:protein ste5;
PDBTitle: solution structure of ste5pm24 in sds micelle

Phyre2
8 |
| c2l4uA_ |

### PDB 2l4u chain A

Region: 129 - 156
Aligned: 22
Modelled: 28
Confidence: 11.8%
Identity: 41%
PDB header:signaling protein
Chain: A: PDB Molecule:24mer peptide from protein ste5;
PDBTitle: solution structure of ste5pm24 in the presence of sds micelle

Phyre2
9 |
| c1xk5A_ |

### PDB 1xk5 chain A

Region: 122 - 129
Aligned: 8
Modelled: 8
Confidence: 9.3%
Identity: 38%
PDB header:transport protein
Chain: A: PDB Molecule:snurportin-1;
PDBTitle: crystal structure of the m3g-cap-binding domain of2 snurportin1 in complex with a m3gpppg-cap dinucleotide

Phyre2
10 |
| d1ukfa_ |

### PDB 1ukf chain A

Region: 21 - 68
Aligned: 47
Modelled: 48
Confidence: 9.0%
Identity: 19%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Avirulence protein Avrpph3

Phyre2
11 |
| d2fcwa1 |

### PDB 2fcw chain A domain 1

Region: 102 - 126
Aligned: 25
Modelled: 25
Confidence: 8.9%
Identity: 32%
Fold: RAP domain-like
Superfamily: RAP domain-like
Family: RAP domain

Phyre2
12 |
| c3gb8B_ |

### PDB 3gb8 chain B

Region: 122 - 129
Aligned: 8
Modelled: 8
Confidence: 8.0%
Identity: 38%
PDB header:transport protein
Chain: B: PDB Molecule:snurportin-1;
PDBTitle: crystal structure of crm1/snurportin-1 complex

Phyre2
13 |
| c3gjxE_ |

### PDB 3gjx chain E

Region: 122 - 129
Aligned: 8
Modelled: 8
Confidence: 7.6%
Identity: 38%
PDB header:protein transport
Chain: E: PDB Molecule:snurportin-1;
PDBTitle: crystal structure of the nuclear export complex crm1-2 snurportin1-rangtp

Phyre2
14 |
| c3h7hA_ |

### PDB 3h7h chain A

Region: 30 - 46
Aligned: 17
Modelled: 17
Confidence: 7.3%
Identity: 41%
PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor spt4;
PDBTitle: crystal structure of the human transcription elongation factor dsif,2 hspt4/hspt5 (176-273)

Phyre2
15 |
| c2zxrA_ |

### PDB 2zxr chain A

Region: 5 - 23
Aligned: 18
Modelled: 19
Confidence: 6.3%
Identity: 44%
PDB header:hydrolase
Chain: A: PDB Molecule:single-stranded dna specific exonuclease recj;
PDBTitle: crystal structure of recj in complex with mg2+ from thermus2 thermophilus hb8

Phyre2
16 |
| d2foka1 |

### PDB 2fok chain A domain 1

Region: 26 - 85
Aligned: 50
Modelled: 60
Confidence: 6.2%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Restriction endonuclease FokI, N-terminal (recognition) domain

Phyre2
17 |
| c1txkA_ |

### PDB 1txk chain A

Region: 109 - 133
Aligned: 25
Modelled: 25
Confidence: 6.2%
Identity: 28%
PDB header:biosynthetic protein
Chain: A: PDB Molecule:glucans biosynthesis protein g;
PDBTitle: crystal structure of escherichia coli opgg

Phyre2
18 |
| d1f44a1 |

### PDB 1f44 chain A domain 1

Region: 99 - 132
Aligned: 33
Modelled: 34
Confidence: 6.1%
Identity: 21%
Fold: SAM domain-like
Superfamily: lambda integrase-like, N-terminal domain
Family: lambda integrase-like, N-terminal domain

Phyre2
19 |
| d1j0sa_ |

### PDB 1j0s chain A

Region: 5 - 46
Aligned: 42
Modelled: 42
Confidence: 6.1%
Identity: 12%
Fold: beta-Trefoil
Superfamily: Cytokine
Family: Interleukin-1 (IL-1)

Phyre2
20 |
| d1txka2 |

### PDB 1txk chain A domain 2

Region: 109 - 133
Aligned: 25
Modelled: 25
Confidence: 6.1%
Identity: 28%
Fold: Supersandwich
Superfamily: Galactose mutarotase-like
Family: MdoG-like

Phyre2
21 |
22 |
23 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3bjqA_ |
|  | 25.0 | 23 | PDB header:viral protein Chain: A: PDB Molecule:phage-related protein; PDBTitle: crystal structure of a phage-related protein (bb3626) from bordetella2 bronchiseptica rb50 at 2.05 a resolution
2 | c2e52A_ |
|  | 20.4 | 26 | PDB header:hydrolase/dna Chain: A: PDB Molecule:type ii restriction enzyme hindiii; PDBTitle: crystal structural analysis of hindiii restriction endonuclease in2 complex with cognate dna at 2.0 angstrom resolution
3 | d1m9za_ |
|  | 18.2 | 12 | Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors
4 | d1ks6a_ |
|  | 18.0 | 29 | Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors
5 | d2pjyb1 |
|  | 17.7 | 12 | Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors
6 | d1ploa_ |
|  | 16.7 | 12 | Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors
7 | c2kgmA_ |
|  | 14.9 | 41 | PDB header:signaling protein Chain: A: PDB Molecule:protein ste5; PDBTitle: solution structure of ste5pm24 in sds micelle
8 | c2l4uA_ |
|  | 11.8 | 41 | PDB header:signaling protein Chain: A: PDB Molecule:24mer peptide from protein ste5; PDBTitle: solution structure of ste5pm24 in the presence of sds micelle
9 | c1xk5A_ |
|  | 9.3 | 38 | PDB header:transport protein Chain: A: PDB Molecule:snurportin-1; PDBTitle: crystal structure of the m3g-cap-binding domain of2 snurportin1 in complex with a m3gpppg-cap dinucleotide
10 | d1ukfa_ |
|  | 9.0 | 19 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Avirulence protein Avrpph3
11 | d2fcwa1 |
|  | 8.9 | 32 | Fold:RAP domain-like Superfamily:RAP domain-like Family:RAP domain
12 | c3gb8B_ |
|  | 8.0 | 38 | PDB header:transport protein Chain: B: PDB Molecule:snurportin-1; PDBTitle: crystal structure of crm1/snurportin-1 complex
13 | c3gjxE_ |
|  | 7.6 | 38 | PDB header:protein transport Chain: E: PDB Molecule:snurportin-1; PDBTitle: crystal structure of the nuclear export complex crm1-2 snurportin1-rangtp
14 | c3h7hA_ |
|  | 7.3 | 41 | PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt4; PDBTitle: crystal structure of the human transcription elongation factor dsif,2 hspt4/hspt5 (176-273)
15 | c2zxrA_ |
|  | 6.3 | 44 | PDB header:hydrolase Chain: A: PDB Molecule:single-stranded dna specific exonuclease recj; PDBTitle: crystal structure of recj in complex with mg2+ from thermus2 thermophilus hb8
16 | d2foka1 |
|  | 6.2 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Restriction endonuclease FokI, N-terminal (recognition) domain
17 | c1txkA_ |
|  | 6.2 | 28 | PDB header:biosynthetic protein Chain: A: PDB Molecule:glucans biosynthesis protein g; PDBTitle: crystal structure of escherichia coli opgg
18 | d1f44a1 |
|  | 6.1 | 21 | Fold:SAM domain-like Superfamily:lambda integrase-like, N-terminal domain Family:lambda integrase-like, N-terminal domain
19 | d1j0sa_ |
|  | 6.1 | 12 | Fold:beta-Trefoil Superfamily:Cytokine Family:Interleukin-1 (IL-1)
20 | d1txka2 |
|  | 6.1 | 28 | Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:MdoG-like
21 | d2ftua1 |
| not modelled | 6.0 | 32 | Fold:RAP domain-like Superfamily:RAP domain-like Family:RAP domain
22 | c2kgnA_ |
| not modelled | 6.0 | 41 | PDB header:signaling protein Chain: A: PDB Molecule:protein ste5; PDBTitle: solution structure of ste5pm24 in the zwitterionic dpc2 micelle
23 | c2hyiJ_ |
| not modelled | 5.7 | 29 | PDB header:hydrolase/rna binding protein/rna Chain: J: PDB Molecule:protein casc3; PDBTitle: structure of the human exon junction complex with a trapped2 dead-box helicase bound to rna

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