Phyre 2 Results for P77759

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Email | l.a.kelley@imperial.ac.uk
Description | P77759
Date | Thu Jan 5 12:32:39 GMT 2012
Unique Job ID | 18b726f7d280ebf6

Summary |

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

Model (left) based on template d1x3za1
Top template information
Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core
Confidence and coverage
Confidence: | 18.3% | Coverage: | 14%
34 residues ( 14% of your sequence) have been modelled with 18.3% 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 | L | A | L | M | D | A | D | G | N | I | A | W | S | G | E | Y | D | E | W | G | N | Q | L | N | E | E | N | P | H | H | L | H | Q | P | Y | R | L | P | G | Q | Q | Y | D | K | E | S | G | L | Y | Y | N | R | N | R | Y | Y | D | P | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | G | R | Y | I | T | Q | D | P | I | G | L | E | G | G | W | S | L | Y | A | Y | P | L | N | P | V | N | G | I | D | P | L | G | L | S | P | A | D | V | A | L | I | R | R | K | D | Q | L | N | H | Q | R | A | W | D | I | L | S | D | T
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | Y | E | D | M | K | R | L | N | L | G | G | T | D | Q | F | F | H | C | M | A | F | C | R | V | S | K | L | N | D | A | G | V | S | R | S | A | K | G | L | G | Y | E | K | E | I | R | D | Y | G | L | N | L | F | G | M | Y | G | R | K | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  | ? |  |  |  |  |  |  | ? |  |  |  |  | ? |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  | ? |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | .
Sequence |  | K | L | S | H | S | E | M | I | E | D | N | K | K | D | L | A | V | N | D | H | G | L | T | C | P | S | T | T | D | C | S | D | R | C | S | D | Y | I | N | P | E | H | K | K | T | I | K | A | L | Q | D | A | G | Y | L | 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 |
| d1x3za1 |

### PDB 1x3z chain A domain 1

Region: 56 - 89
Aligned: 34
Modelled: 34
Confidence: 18.3%
Identity: 12%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Transglutaminase core

Phyre2
2 |
| d2f4ma1 |

### PDB 2f4m chain A domain 1

Region: 56 - 89
Aligned: 34
Modelled: 34
Confidence: 13.2%
Identity: 24%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Transglutaminase core

Phyre2
3 |
| d1c3ha_ |

### PDB 1c3h chain A

Region: 57 - 69
Aligned: 13
Modelled: 13
Confidence: 7.6%
Identity: 31%
Fold: TNF-like
Superfamily: TNF-like
Family: TNF-like

Phyre2
4 |
| c3m1hB_ |

### PDB 3m1h chain B

Region: 38 - 70
Aligned: 33
Modelled: 33
Confidence: 6.5%
Identity: 15%
PDB header:cell invasion
Chain: B: PDB Molecule:lysine specific cysteine protease;
PDBTitle: crystal structure analysis of the k3 cleaved adhesin domain of lys-2 gingipain (kgp) from porphyromonas gingivalis w83

Phyre2
5 |
| c3eswA_ |

### PDB 3esw chain A

Region: 56 - 69
Aligned: 14
Modelled: 14
Confidence: 5.8%
Identity: 21%
PDB header:hydrolase
Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine
PDBTitle: complex of yeast pngase with glcnac2-iac.

Phyre2
6 |
| c2ka3C_ |

### PDB 2ka3 chain C

Region: 57 - 69
Aligned: 13
Modelled: 13
Confidence: 5.7%
Identity: 31%
PDB header:structural protein
Chain: C: PDB Molecule:emilin-1;
PDBTitle: structure of emilin-1 c1q-like domain

Phyre2
7 |
| d1zaka2 |

### PDB 1zak chain A domain 2

Region: 40 - 51
Aligned: 12
Modelled: 12
Confidence: 5.6%
Identity: 33%
Fold: Rubredoxin-like
Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
Family: Microbial and mitochondrial ADK, insert "zinc finger" domain

Phyre2
8 |
| d1m3ya2 |

### PDB 1m3y chain A domain 2

Region: 75 - 93
Aligned: 18
Modelled: 19
Confidence: 5.6%
Identity: 39%
Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily: Group II dsDNA viruses VP
Family: Major capsid protein vp54

Phyre2
9 |
| d1bcoa1 |

### PDB 1bco chain A domain 1

Region: 48 - 65
Aligned: 18
Modelled: 18
Confidence: 5.1%
Identity: 22%
Fold: mu transposase, C-terminal domain
Superfamily: mu transposase, C-terminal domain
Family: mu transposase, C-terminal domain

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1x3za1 |
|  | 18.3 | 12 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core
2 | d2f4ma1 |
|  | 13.2 | 24 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core
3 | d1c3ha_ |
|  | 7.6 | 31 | Fold:TNF-like Superfamily:TNF-like Family:TNF-like
4 | c3m1hB_ |
|  | 6.5 | 15 | PDB header:cell invasion Chain: B: PDB Molecule:lysine specific cysteine protease; PDBTitle: crystal structure analysis of the k3 cleaved adhesin domain of lys-2 gingipain (kgp) from porphyromonas gingivalis w83
5 | c3eswA_ |
|  | 5.8 | 21 | PDB header:hydrolase Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine PDBTitle: complex of yeast pngase with glcnac2-iac.
6 | c2ka3C_ |
|  | 5.7 | 31 | PDB header:structural protein Chain: C: PDB Molecule:emilin-1; PDBTitle: structure of emilin-1 c1q-like domain
7 | d1zaka2 |
|  | 5.6 | 33 | Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
8 | d1m3ya2 |
|  | 5.6 | 39 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Major capsid protein vp54
9 | d1bcoa1 |
|  | 5.1 | 22 | Fold:mu transposase, C-terminal domain Superfamily:mu transposase, C-terminal domain Family:mu transposase, C-terminal domain

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