Phyre 2 Results for Q46919

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Email | l.a.kelley@imperial.ac.uk
Description | Q46919
Date | Thu Jan 5 12:35:52 GMT 2012
Unique Job ID | 2c79acea5338904f

Summary |

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

Model (left) based on template d2hgka1
Top template information
Fold:Bromodomain-like Superfamily:YqcC-like Family:YqcC-like
Confidence and coverage
Confidence: | 100.0% | Coverage: | 100%
109 residues (100% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | T | T | H | D | R | V | R | L | Q | L | Q | A | L | E | A | L | L | R | E | H | Q | H | W | R | N | D | E | P | Q | P | H | Q | F | N | S | T | Q | P | F | F | M | D | T | M | E | P | L | E | W | L | Q | W | V | L | I | P | R | M | H
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  | ? | ? |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | .
Sequence |  | D | L | L | D | N | K | Q | P | L | P | G | A | F | A | V | A | P | Y | Y | E | M | A | L | A | T | D | H | P | Q | R | A | L | I | L | A | E | L | E | K | L | D | A | L | F | A | D | D | A | S
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 |
| d2hgka1 |

### PDB 2hgk chain A domain 1

Region: 1 - 109
Aligned: 109
Modelled: 109
Confidence: 100.0%
Identity: 100%
Fold: Bromodomain-like
Superfamily: YqcC-like
Family: YqcC-like

Phyre2
2 |
| c2gc6A_ |

### PDB 2gc6 chain A

Region: 45 - 64
Aligned: 20
Modelled: 20
Confidence: 31.5%
Identity: 30%
PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase;
PDBTitle: s73a mutant of l. casei fpgs

Phyre2
3 |
| c3d1dC_ |

### PDB 3d1d chain C

Region: 18 - 71
Aligned: 54
Modelled: 54
Confidence: 17.4%
Identity: 17%
PDB header:nuclear protein
Chain: C: PDB Molecule:rna-induced transcriptional silencing complex
PDBTitle: hexagonal crystal structure of tas3 c-terminal alpha motif

Phyre2
4 |
| d1ewfa2 |

### PDB 1ewf chain A domain 2

Region: 51 - 75
Aligned: 25
Modelled: 25
Confidence: 17.1%
Identity: 28%
Fold: Aha1/BPI domain-like
Superfamily: Bactericidal permeability-increasing protein, BPI
Family: Bactericidal permeability-increasing protein, BPI

Phyre2
5 |
| d1eswa_ |

### PDB 1esw chain A

Region: 43 - 64
Aligned: 22
Modelled: 22
Confidence: 16.5%
Identity: 14%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: Amylase, catalytic domain

Phyre2
6 |
| d1w1oa1 |

### PDB 1w1o chain A domain 1

Region: 2 - 29
Aligned: 28
Modelled: 28
Confidence: 15.0%
Identity: 18%
Fold: Ferredoxin-like
Superfamily: FAD-linked oxidases, C-terminal domain
Family: Cytokinin dehydrogenase 1

Phyre2
7 |
| c2yu0A_ |

### PDB 2yu0 chain A

Region: 71 - 103
Aligned: 32
Modelled: 33
Confidence: 11.1%
Identity: 19%
PDB header:signaling protein
Chain: A: PDB Molecule:interferon-activable protein 205;
PDBTitle: solution structures of the paad_dapin domain of mus2 musculus interferon-activatable protein 205

Phyre2
8 |
| c1bp1A_ |

### PDB 1bp1 chain A

Region: 51 - 75
Aligned: 25
Modelled: 25
Confidence: 9.7%
Identity: 28%
PDB header:bactericidal
Chain: A: PDB Molecule:bactericidal/permeability-increasing protein;
PDBTitle: crystal structure of bpi, the human bactericidal2 permeability-increasing protein

Phyre2
9 |
| d1x1na1 |

### PDB 1x1n chain A domain 1

Region: 43 - 64
Aligned: 22
Modelled: 22
Confidence: 9.4%
Identity: 14%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: Amylase, catalytic domain

Phyre2
10 |
| d2gc6a2 |

### PDB 2gc6 chain A domain 2

Region: 45 - 64
Aligned: 20
Modelled: 20
Confidence: 9.3%
Identity: 30%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: Folylpolyglutamate synthetase

Phyre2
11 |
| d1tz7a1 |

### PDB 1tz7 chain A domain 1

Region: 43 - 64
Aligned: 22
Modelled: 22
Confidence: 8.7%
Identity: 14%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: Amylase, catalytic domain

Phyre2
12 |
| d1jb0i_ |

### PDB 1jb0 chain I

Region: 51 - 59
Aligned: 9
Modelled: 9
Confidence: 7.8%
Identity: 44%
Fold: Single transmembrane helix
Superfamily: Subunit VIII of photosystem I reaction centre, PsaI
Family: Subunit VIII of photosystem I reaction centre, PsaI

Phyre2
13 |
| c1pnbB_ |

### PDB 1pnb chain B

Region: 59 - 77
Aligned: 19
Modelled: 19
Confidence: 7.5%
Identity: 11%
PDB header:seed storage protein
Chain: B: PDB Molecule:napin bnib;
PDBTitle: structure of napin bnib, nmr, 10 structures

Phyre2
14 |
| c3if4C_ |

### PDB 3if4 chain C

Region: 46 - 55
Aligned: 10
Modelled: 10
Confidence: 6.9%
Identity: 30%
PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:integron cassette protein hfx_cass5;
PDBTitle: structure from the mobile metagenome of north west arm2 sewage outfall: integron cassette protein hfx_cass5

Phyre2
15 |
| d1v38a_ |

### PDB 1v38 chain A

Region: 48 - 109
Aligned: 61
Modelled: 62
Confidence: 6.1%
Identity: 13%
Fold: SAM domain-like
Superfamily: SAM/Pointed domain
Family: SAM (sterile alpha motif) domain

Phyre2
16 |
| d2r7ga2 |

### PDB 2r7g chain A domain 2

Region: 54 - 63
Aligned: 10
Modelled: 10
Confidence: 5.6%
Identity: 20%
Fold: Cyclin-like
Superfamily: Cyclin-like
Family: Retinoblastoma tumor suppressor domains

Phyre2
17 |
| c3k1qA_ |

### PDB 3k1q chain A

Region: 40 - 64
Aligned: 24
Modelled: 25
Confidence: 5.6%
Identity: 13%
PDB header:virus
Chain: A: PDB Molecule:vp1, the protein that forms the mrna-capping
PDBTitle: backbone model of an aquareovirus virion by cryo-electron2 microscopy and bioinformatics

Phyre2
18 |
| d2fgea3 |

### PDB 2fge chain A domain 3

Region: 9 - 36
Aligned: 28
Modelled: 28
Confidence: 5.3%
Identity: 14%
Fold: LuxS/MPP-like metallohydrolase
Superfamily: LuxS/MPP-like metallohydrolase
Family: MPP-like

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2hgka1 |
|  | 100.0 | 100 | Fold:Bromodomain-like Superfamily:YqcC-like Family:YqcC-like
2 | c2gc6A_ |
|  | 31.5 | 30 | PDB header:ligase Chain: A: PDB Molecule:folylpolyglutamate synthase; PDBTitle: s73a mutant of l. casei fpgs
3 | c3d1dC_ |
|  | 17.4 | 17 | PDB header:nuclear protein Chain: C: PDB Molecule:rna-induced transcriptional silencing complex PDBTitle: hexagonal crystal structure of tas3 c-terminal alpha motif
4 | d1ewfa2 |
|  | 17.1 | 28 | Fold:Aha1/BPI domain-like Superfamily:Bactericidal permeability-increasing protein, BPI Family:Bactericidal permeability-increasing protein, BPI
5 | d1eswa_ |
|  | 16.5 | 14 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
6 | d1w1oa1 |
|  | 15.0 | 18 | Fold:Ferredoxin-like Superfamily:FAD-linked oxidases, C-terminal domain Family:Cytokinin dehydrogenase 1
7 | c2yu0A_ |
|  | 11.1 | 19 | PDB header:signaling protein Chain: A: PDB Molecule:interferon-activable protein 205; PDBTitle: solution structures of the paad_dapin domain of mus2 musculus interferon-activatable protein 205
8 | c1bp1A_ |
|  | 9.7 | 28 | PDB header:bactericidal Chain: A: PDB Molecule:bactericidal/permeability-increasing protein; PDBTitle: crystal structure of bpi, the human bactericidal2 permeability-increasing protein
9 | d1x1na1 |
|  | 9.4 | 14 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
10 | d2gc6a2 |
|  | 9.3 | 30 | Fold:Ribokinase-like Superfamily:MurD-like peptide ligases, catalytic domain Family:Folylpolyglutamate synthetase
11 | d1tz7a1 |
|  | 8.7 | 14 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
12 | d1jb0i_ |
|  | 7.8 | 44 | Fold:Single transmembrane helix Superfamily:Subunit VIII of photosystem I reaction centre, PsaI Family:Subunit VIII of photosystem I reaction centre, PsaI
13 | c1pnbB_ |
|  | 7.5 | 11 | PDB header:seed storage protein Chain: B: PDB Molecule:napin bnib; PDBTitle: structure of napin bnib, nmr, 10 structures
14 | c3if4C_ |
|  | 6.9 | 30 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:integron cassette protein hfx_cass5; PDBTitle: structure from the mobile metagenome of north west arm2 sewage outfall: integron cassette protein hfx_cass5
15 | d1v38a_ |
|  | 6.1 | 13 | Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain
16 | d2r7ga2 |
|  | 5.6 | 20 | Fold:Cyclin-like Superfamily:Cyclin-like Family:Retinoblastoma tumor suppressor domains
17 | c3k1qA_ |
|  | 5.6 | 13 | PDB header:virus Chain: A: PDB Molecule:vp1, the protein that forms the mrna-capping PDBTitle: backbone model of an aquareovirus virion by cryo-electron2 microscopy and bioinformatics
18 | d2fgea3 |
|  | 5.3 | 14 | Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:MPP-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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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