Phyre 2 Results for P37757

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Email | l.a.kelley@imperial.ac.uk
Description | P37757
Date | Thu Jan 5 11:57:29 GMT 2012
Unique Job ID | 846e28bc1a63b25d

Summary |

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

Model (left) based on template c1qy9B_
Top template information
PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein ydde; PDBTitle: crystal structure of e. coli se-met protein ydde
Confidence and coverage
Confidence: | 100.0% | Coverage: | 99%
295 residues ( 99% 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 | K | P | Q | V | Y | H | V | D | A | F | T | S | Q | P | F | R | G | N | S | A | G | V | V | F | P | A | D | N | L | S | E | A | Q | M | Q | L | I | A | R | E | L | G | H | S | E | T | A | F | L | L | H | S | D | D | S | D | V | R | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | R | Y | F | T | P | T | V | E | V | P | I | C | G | H | A | T | V | A | A | H | Y | V | R | A | K | V | L | G | L | G | N | C | T | I | W | Q | T | S | L | A | G | K | H | R | V | T | I | E | K | H | N | D | D | Y | R | I | S | L | E | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | G | T | P | G | F | E | P | P | L | E | G | E | T | R | A | A | I | I | N | A | L | H | L | T | E | D | D | I | L | P | G | L | P | I | Q | V | A | T | T | G | H | S | K | V | M | I | P | L | K | P | E | V | D | I | D | A | L | S | P | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | L | N | A | L | T | A | I | S | K | K | I | G | C | N | G | F | F | P | F | Q | I | R | P | G | K | N | E | T | D | G | R | M | F | S | P | A | I | G | I | V | E | D | P | V | T | G | N | A | N | G | P | M | G | A | W | L | V | H | H | N
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | .
Sequence |  | V | L | P | H | D | G | N | V | L | R | V | K | G | H | Q | G | R | A | L | G | R | D | G | M | I | E | V | T | V | T | I | R | D | N | Q | P | E | K | V | T | I | S | G | T | A | V | I | L | F | H | A | E | W | A | I | E | L
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 |
| c1qy9B_ |

### PDB 1qy9 chain B

Region: 3 - 297
Aligned: 295
Modelled: 295
Confidence: 100.0%
Identity: 98%
PDB header:unknown function
Chain: B: PDB Molecule:hypothetical protein ydde;
PDBTitle: crystal structure of e. coli se-met protein ydde

Phyre2
2 |
| c3ednB_ |

### PDB 3edn chain B

Region: 2 - 295
Aligned: 291
Modelled: 294
Confidence: 100.0%
Identity: 32%
PDB header:biosynthetic protein
Chain: B: PDB Molecule:phenazine biosynthesis protein, phzf family;
PDBTitle: crystal structure of the bacillus anthracis phenazine2 biosynthesis protein, phzf family

Phyre2
3 |
| c1ym5A_ |

### PDB 1ym5 chain A

Region: 1 - 295
Aligned: 282
Modelled: 295
Confidence: 100.0%
Identity: 23%
PDB header:oxidoreductase
Chain: A: PDB Molecule:hypothetical 32.6 kda protein in dap2-slt2
PDBTitle: crystal structure of yhi9, the yeast member of the2 phenazine biosynthesis phzf enzyme superfamily.

Phyre2
4 |
| c1u1wA_ |

### PDB 1u1w chain A

Region: 2 - 295
Aligned: 276
Modelled: 294
Confidence: 100.0%
Identity: 30%
PDB header:isomerase, lyase
Chain: A: PDB Molecule:phenazine biosynthesis protein phzf;
PDBTitle: structure and function of phenazine-biosynthesis protein phzf from2 pseudomonas fluorescens 2-79

Phyre2
5 |
| c1u0kA_ |

### PDB 1u0k chain A

Region: 1 - 294
Aligned: 279
Modelled: 288
Confidence: 100.0%
Identity: 25%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:gene product pa4716;
PDBTitle: the structure of a predicted epimerase pa4716 from pseudomonas2 aeruginosa

Phyre2
6 |
| d1s7ja_ |

### PDB 1s7j chain A

Region: 1 - 295
Aligned: 260
Modelled: 286
Confidence: 100.0%
Identity: 31%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: PhzC/PhzF-like

Phyre2
7 |
| c3ekmE_ |

### PDB 3ekm chain E

Region: 11 - 295
Aligned: 263
Modelled: 285
Confidence: 100.0%
Identity: 16%
PDB header:isomerase
Chain: E: PDB Molecule:diaminopimelate epimerase, chloroplastic;
PDBTitle: crystal structure of diaminopimelate epimerase form2 arabidopsis thaliana in complex with irreversible inhibitor3 dl-azidap

Phyre2
8 |
| c2otnB_ |

### PDB 2otn chain B

Region: 11 - 297
Aligned: 262
Modelled: 280
Confidence: 100.0%
Identity: 16%
PDB header:isomerase
Chain: B: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal structure of the catalytically active form of diaminopimelate2 epimerase from bacillus anthracis

Phyre2
9 |
| c2gkjA_ |

### PDB 2gkj chain A

Region: 11 - 295
Aligned: 260
Modelled: 285
Confidence: 100.0%
Identity: 15%
PDB header:isomerase
Chain: A: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal structure of diaminopimelate epimerase in complex2 with an irreversible inhibitor dl-azidap

Phyre2
10 |
| c2azpA_ |

### PDB 2azp chain A

Region: 1 - 296
Aligned: 280
Modelled: 295
Confidence: 100.0%
Identity: 14%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa1268;
PDBTitle: crystal structure of pa1268 solved by sulfur sad

Phyre2
11 |
| c1w62B_ |

### PDB 1w62 chain B

Region: 5 - 296
Aligned: 286
Modelled: 292
Confidence: 100.0%
Identity: 13%
PDB header:racemase
Chain: B: PDB Molecule:b-cell mitogen;
PDBTitle: proline racemase in complex with one molecule of pyrrole-2-2 carboxylic acid (hemi form)

Phyre2
12 |
| d1qy9a1 |

### PDB 1qy9 chain A domain 1

Region: 3 - 129
Aligned: 127
Modelled: 127
Confidence: 100.0%
Identity: 99%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: PhzC/PhzF-like

Phyre2
13 |
| c3fveA_ |

### PDB 3fve chain A

Region: 11 - 293
Aligned: 244
Modelled: 263
Confidence: 100.0%
Identity: 16%
PDB header:isomerase
Chain: A: PDB Molecule:diaminopimelate epimerase;
PDBTitle: crystal structure of diaminopimelate epimerase mycobacterium2 tuberculosis dapf

Phyre2
14 |
| d1u0ka1 |

### PDB 1u0k chain A domain 1

Region: 3 - 127
Aligned: 125
Modelled: 125
Confidence: 100.0%
Identity: 26%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: PhzC/PhzF-like

Phyre2
15 |
| d1xuba1 |

### PDB 1xub chain A domain 1

Region: 1 - 127
Aligned: 124
Modelled: 126
Confidence: 100.0%
Identity: 33%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: PhzC/PhzF-like

Phyre2
16 |
| d1qy9a2 |

### PDB 1qy9 chain A domain 2

Region: 132 - 297
Aligned: 166
Modelled: 166
Confidence: 100.0%
Identity: 98%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: PhzC/PhzF-like

Phyre2
17 |
| d1tm0a_ |

### PDB 1tm0 chain A

Region: 5 - 296
Aligned: 265
Modelled: 283
Confidence: 100.0%
Identity: 14%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: Proline racemase

Phyre2
18 |
| d1xuba2 |

### PDB 1xub chain A domain 2

Region: 135 - 295
Aligned: 148
Modelled: 155
Confidence: 100.0%
Identity: 30%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: PhzC/PhzF-like

Phyre2
19 |
| d1u0ka2 |

### PDB 1u0k chain A domain 2

Region: 135 - 293
Aligned: 144
Modelled: 159
Confidence: 99.9%
Identity: 30%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: PhzC/PhzF-like

Phyre2
20 |
| d2gkea1 |

### PDB 2gke chain A domain 1

Region: 11 - 132
Aligned: 118
Modelled: 122
Confidence: 99.9%
Identity: 20%
Fold: Diaminopimelate epimerase-like
Superfamily: Diaminopimelate epimerase-like
Family: Diaminopimelate epimerase

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1qy9B_ |
|  | 100.0 | 98 | PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein ydde; PDBTitle: crystal structure of e. coli se-met protein ydde
2 | c3ednB_ |
|  | 100.0 | 32 | PDB header:biosynthetic protein Chain: B: PDB Molecule:phenazine biosynthesis protein, phzf family; PDBTitle: crystal structure of the bacillus anthracis phenazine2 biosynthesis protein, phzf family
3 | c1ym5A_ |
|  | 100.0 | 23 | PDB header:oxidoreductase Chain: A: PDB Molecule:hypothetical 32.6 kda protein in dap2-slt2 PDBTitle: crystal structure of yhi9, the yeast member of the2 phenazine biosynthesis phzf enzyme superfamily.
4 | c1u1wA_ |
|  | 100.0 | 30 | PDB header:isomerase, lyase Chain: A: PDB Molecule:phenazine biosynthesis protein phzf; PDBTitle: structure and function of phenazine-biosynthesis protein phzf from2 pseudomonas fluorescens 2-79
5 | c1u0kA_ |
|  | 100.0 | 25 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:gene product pa4716; PDBTitle: the structure of a predicted epimerase pa4716 from pseudomonas2 aeruginosa
6 | d1s7ja_ |
|  | 100.0 | 31 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like
7 | c3ekmE_ |
|  | 100.0 | 16 | PDB header:isomerase Chain: E: PDB Molecule:diaminopimelate epimerase, chloroplastic; PDBTitle: crystal structure of diaminopimelate epimerase form2 arabidopsis thaliana in complex with irreversible inhibitor3 dl-azidap
8 | c2otnB_ |
|  | 100.0 | 16 | PDB header:isomerase Chain: B: PDB Molecule:diaminopimelate epimerase; PDBTitle: crystal structure of the catalytically active form of diaminopimelate2 epimerase from bacillus anthracis
9 | c2gkjA_ |
|  | 100.0 | 15 | PDB header:isomerase Chain: A: PDB Molecule:diaminopimelate epimerase; PDBTitle: crystal structure of diaminopimelate epimerase in complex2 with an irreversible inhibitor dl-azidap
10 | c2azpA_ |
|  | 100.0 | 14 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa1268; PDBTitle: crystal structure of pa1268 solved by sulfur sad
11 | c1w62B_ |
|  | 100.0 | 13 | PDB header:racemase Chain: B: PDB Molecule:b-cell mitogen; PDBTitle: proline racemase in complex with one molecule of pyrrole-2-2 carboxylic acid (hemi form)
12 | d1qy9a1 |
|  | 100.0 | 99 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like
13 | c3fveA_ |
|  | 100.0 | 16 | PDB header:isomerase Chain: A: PDB Molecule:diaminopimelate epimerase; PDBTitle: crystal structure of diaminopimelate epimerase mycobacterium2 tuberculosis dapf
14 | d1u0ka1 |
|  | 100.0 | 26 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like
15 | d1xuba1 |
|  | 100.0 | 33 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like
16 | d1qy9a2 |
|  | 100.0 | 98 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like
17 | d1tm0a_ |
|  | 100.0 | 14 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:Proline racemase
18 | d1xuba2 |
|  | 100.0 | 30 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like
19 | d1u0ka2 |
|  | 99.9 | 30 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like
20 | d2gkea1 |
|  | 99.9 | 20 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:Diaminopimelate epimerase
21 | d2gkea2 |
| not modelled | 99.8 | 13 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:Diaminopimelate epimerase
22 | c3g7kD_ |
| not modelled | 98.2 | 16 | PDB header:isomerase Chain: D: PDB Molecule:3-methylitaconate isomerase; PDBTitle: crystal structure of methylitaconate-delta-isomerase
23 | c2pw0A_ |
| not modelled | 98.1 | 18 | PDB header:unknown function Chain: A: PDB Molecule:prpf methylaconitate isomerase; PDBTitle: crystal structure of trans-aconitate bound to methylaconitate2 isomerase prpf from shewanella oneidensis
24 | d2h9fa2 |
| not modelled | 96.0 | 23 | Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PA0793-like
25 | c3ldgA_ |
| not modelled | 40.2 | 18 | PDB header:transferase Chain: A: PDB Molecule:putative uncharacterized protein smu.472; PDBTitle: crystal structure of smu.472, a putative methyltransferase complexed2 with sah
26 | c3k0bA_ |
| not modelled | 38.8 | 18 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted n6-adenine-specific dna methylase; PDBTitle: crystal structure of a predicted n6-adenine-specific dna methylase2 from listeria monocytogenes str. 4b f2365
27 | d1g60a_ |
| not modelled | 36.5 | 19 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Type II DNA methylase
28 | d1booa_ |
| not modelled | 33.8 | 13 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Type II DNA methylase
29 | c2zifB_ |
| not modelled | 32.7 | 23 | PDB header:transferase Chain: B: PDB Molecule:putative modification methylase; PDBTitle: crystal structure of ttha0409, putative dna modification2 methylase from thermus thermophilus hb8- complexed with s-3 adenosyl-l-methionine
30 | d1euza2 |
| not modelled | 31.7 | 26 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
31 | d1bgva2 |
| not modelled | 31.5 | 19 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
32 | d1v9la2 |
| not modelled | 31.0 | 19 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
33 | c1nw6A_ |
| not modelled | 29.6 | 19 | PDB header:transferase Chain: A: PDB Molecule:modification methylase rsri; PDBTitle: structure of the beta class n6-adenine dna methyltransferase rsri2 bound to sinefungin
34 | d1o9ga_ |
| not modelled | 28.7 | 27 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:rRNA methyltransferase AviRa
35 | d1gtma2 |
| not modelled | 26.6 | 23 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
36 | d1eg2a_ |
| not modelled | 24.2 | 17 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Type II DNA methylase
37 | c3lduA_ |
| not modelled | 23.6 | 26 | PDB header:transferase Chain: A: PDB Molecule:putative methylase; PDBTitle: the crystal structure of a possible methylase from2 clostridium difficile 630.
38 | d1bvua2 |
| not modelled | 23.4 | 23 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
39 | d2ar0a1 |
| not modelled | 22.3 | 36 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:N-6 DNA Methylase-like
40 | d2fug21 |
| not modelled | 21.7 | 14 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:NQO2-like
41 | d1b26a2 |
| not modelled | 21.7 | 26 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
42 | c2waqG_ |
| not modelled | 20.6 | 27 | PDB header:transcription Chain: G: PDB Molecule:dna-directed rna polymerase rpo8 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase
43 | c3khkA_ |
| not modelled | 20.2 | 21 | PDB header:dna binding protein Chain: A: PDB Molecule:type i restriction-modification system PDBTitle: crystal structure of type-i restriction-modification system2 methylation subunit (mm_0429) from methanosarchina mazei.
44 | d1hwxa2 |
| not modelled | 19.3 | 29 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
45 | d2okca1 |
| not modelled | 17.8 | 29 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:N-6 DNA Methylase-like
46 | c2l3bA_ |
| not modelled | 17.4 | 33 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein found in conjugate transposon; PDBTitle: solution nmr structure of the bt_0084 lipoprotein from bacteroides2 thetaiotaomicron, northeast structural genomics consortium target3 btr376
47 | d2f8la1 |
| not modelled | 17.2 | 36 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:N-6 DNA Methylase-like
48 | c2l7qA_ |
| not modelled | 16.3 | 27 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein found in conjugate transposon; PDBTitle: solution nmr structure of conjugate transposon protein bvu_1572(27-2 141) from bacteroides vulgatus, northeast structural genomics3 consortium target bvr155
49 | c3p9nA_ |
| not modelled | 16.1 | 21 | PDB header:transferase Chain: A: PDB Molecule:possible methyltransferase (methylase); PDBTitle: rv2966c of m. tuberculosis is a rsmd-like methyltransferase
50 | c1g38A_ |
| not modelled | 15.4 | 7 | PDB header:transferase/dna Chain: A: PDB Molecule:modification methylase taqi; PDBTitle: adenine-specific methyltransferase m. taq i/dna complex
51 | c3sb1B_ |
| not modelled | 15.4 | 23 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hydrogenase expression protein; PDBTitle: hydrogenase expression protein huph from thiobacillus denitrificans2 atcc 25259
52 | c1aqjB_ |
| not modelled | 15.4 | 7 | PDB header:methyltransferase Chain: B: PDB Molecule:adenine-n6-dna-methyltransferase taqi; PDBTitle: structure of adenine-n6-dna-methyltransferase taqi
53 | d1uhsa_ |
| not modelled | 15.2 | 35 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
54 | d2ih2a1 |
| not modelled | 14.0 | 7 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:DNA methylase TaqI, N-terminal domain
55 | d1l1fa2 |
| not modelled | 14.0 | 29 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
56 | c3lkdB_ |
| not modelled | 13.5 | 21 | PDB header:transferase Chain: B: PDB Molecule:type i restriction-modification system PDBTitle: crystal structure of the type i restriction-modification2 system methyltransferase subunit from streptococcus3 thermophilus, northeast structural genomics consortium4 target sur80
57 | d1s7ea1 |
| not modelled | 13.2 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
58 | d1j6ua1 |
| not modelled | 13.1 | 12 | Fold:MurCD N-terminal domain Superfamily:MurCD N-terminal domain Family:MurCD N-terminal domain
59 | d1ko7a1 |
| not modelled | 13.1 | 13 | Fold:MurF and HprK N-domain-like Superfamily:HprK N-terminal domain-like Family:HPr kinase/phoshatase HprK N-terminal domain
60 | d2p81a1 |
| not modelled | 12.2 | 41 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
61 | c3itcA_ |
| not modelled | 12.2 | 13 | PDB header:hydrolase Chain: A: PDB Molecule:renal dipeptidase; PDBTitle: crystal structure of sco3058 with bound citrate and glycerol
62 | c3k8zD_ |
| not modelled | 11.8 | 19 | PDB header:oxidoreductase Chain: D: PDB Molecule:nad-specific glutamate dehydrogenase; PDBTitle: crystal structure of gudb1 a decryptified secondary glutamate2 dehydrogenase from b. subtilis
63 | d1pjza_ |
| not modelled | 11.7 | 24 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Thiopurine S-methyltransferase
64 | c3c6vB_ |
| not modelled | 11.2 | 15 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable tautomerase/dehalogenase au4130; PDBTitle: crystal structure of au4130/apc7354, a probable enzyme from the2 thermophilic fungus aspergillus fumigatus
65 | c1v9lA_ |
| not modelled | 11.0 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:glutamate dehydrogenase; PDBTitle: l-glutamate dehydrogenase from pyrobaculum islandicum2 complexed with nad
66 | d1e3oc1 |
| not modelled | 11.0 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
67 | d1knxa1 |
| not modelled | 10.9 | 3 | Fold:MurF and HprK N-domain-like Superfamily:HprK N-terminal domain-like Family:HPr kinase/phoshatase HprK N-terminal domain
68 | d1wy7a1 |
| not modelled | 10.8 | 33 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Ta1320-like
69 | c2i5gB_ |
| not modelled | 10.6 | 23 | PDB header:hydrolase Chain: B: PDB Molecule:amidohydrolase; PDBTitle: crystal strcuture of amidohydrolase from pseudomonas2 aeruginosa
70 | c1bvuF_ |
| not modelled | 10.4 | 23 | PDB header:oxidoreductase Chain: F: PDB Molecule:protein (glutamate dehydrogenase); PDBTitle: glutamate dehydrogenase from thermococcus litoralis
71 | c2vi6F_ |
| not modelled | 10.3 | 41 | PDB header:transcription Chain: F: PDB Molecule:homeobox protein nanog; PDBTitle: crystal structure of the nanog homeodomain
72 | c2da4A_ |
| not modelled | 10.3 | 18 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein dkfzp686k21156; PDBTitle: solution structure of the homeobox domain of the2 hypothetical protein, dkfzp686k21156
73 | c3lu2B_ |
| not modelled | 10.2 | 14 | PDB header:hydrolase Chain: B: PDB Molecule:lmo2462 protein; PDBTitle: structure of lmo2462, a listeria monocytogenes amidohydrolase family2 putative dipeptidase
74 | d1o4xa1 |
| not modelled | 10.1 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
75 | c3s1sA_ |
| not modelled | 10.0 | 29 | PDB header:hydrolase, transferase Chain: A: PDB Molecule:restriction endonuclease bpusi; PDBTitle: characterization and crystal structure of the type iig restriction2 endonuclease bpusi
76 | d1p7ia_ |
| not modelled | 9.8 | 41 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
77 | c2da2A_ |
| not modelled | 9.7 | 5 | PDB header:transcription Chain: A: PDB Molecule:alpha-fetoprotein enhancer binding protein; PDBTitle: solution structure of the second homeobox domain of at-2 binding transcription factor 1 (atbf1)
78 | c2tmgD_ |
| not modelled | 9.5 | 26 | PDB header:oxidoreductase Chain: D: PDB Molecule:protein (glutamate dehydrogenase); PDBTitle: thermotoga maritima glutamate dehydrogenase mutant s128r,2 t158e, n117r, s160e
79 | d1ne2a_ |
| not modelled | 9.4 | 36 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Ta1320-like
80 | d2hi3a1 |
| not modelled | 9.3 | 35 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
81 | d1ws6a1 |
| not modelled | 9.3 | 29 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:YhhF-like
82 | c2da1A_ |
| not modelled | 9.2 | 29 | PDB header:transcription Chain: A: PDB Molecule:alpha-fetoprotein enhancer binding protein; PDBTitle: solution structure of the first homeobox domain of at-2 binding transcription factor 1 (atbf1)
83 | d2ifta1 |
| not modelled | 9.0 | 21 | Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:YhhF-like
84 | c2yfqA_ |
| not modelled | 9.0 | 23 | PDB header:oxidoreductase Chain: A: PDB Molecule:nad-specific glutamate dehydrogenase; PDBTitle: crystal structure of glutamate dehydrogenase from2 peptoniphilus asaccharolyticus
85 | c2l9rA_ |
| not modelled | 8.9 | 29 | PDB header:transcription Chain: A: PDB Molecule:homeobox protein nkx-3.1; PDBTitle: solution nmr structure of homeobox domain of homeobox protein nkx-3.12 from homo sapiens, northeast structural genomics consortium target3 hr6470a
86 | d2cqxa1 |
| not modelled | 8.8 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
87 | c2ragB_ |
| not modelled | 8.8 | 27 | PDB header:hydrolase Chain: B: PDB Molecule:dipeptidase; PDBTitle: crystal structure of aminohydrolase from caulobacter crescentus
88 | d2cuea1 |
| not modelled | 8.7 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
89 | c3aogA_ |
| not modelled | 8.7 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:glutamate dehydrogenase; PDBTitle: crystal structure of glutamate dehydrogenase (gdhb) from thermus2 thermophilus (glu bound form)
90 | d1au7a1 |
| not modelled | 8.6 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
91 | c2dmuA_ |
| not modelled | 8.5 | 15 | PDB header:dna binding protein Chain: A: PDB Molecule:homeobox protein goosecoid; PDBTitle: solution structure of the homeobox domain of homeobox2 protein goosecoid
92 | d1jgga_ |
| not modelled | 8.5 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
93 | d2j85a1 |
| not modelled | 8.5 | 20 | Fold:STIV B116-like Superfamily:STIV B116-like Family:STIV B116-like
94 | c3fdgA_ |
| not modelled | 8.4 | 27 | PDB header:hydrolase Chain: A: PDB Molecule:dipeptidase ac. metallo peptidase. merops family m19; PDBTitle: the crystal structure of the dipeptidase ac, metallo peptidase. merops2 family m19
95 | d2hddb_ |
| not modelled | 8.1 | 41 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
96 | d1f43a_ |
| not modelled | 8.1 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
97 | d1le8a_ |
| not modelled | 8.0 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
98 | d1ztra1 |
| not modelled | 7.9 | 41 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain
99 | c1ko7B_ |
| not modelled | 7.9 | 13 | PDB header:transferase,hydrolase Chain: B: PDB Molecule:hpr kinase/phosphatase; PDBTitle: x-ray structure of the hpr kinase/phosphatase from2 staphylococcus xylosus at 1.95 a resolution

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