Phyre 2 Results for P29131

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Email | l.a.kelley@imperial.ac.uk
Description | P29131
Date | Thu Jan 5 11:45:35 GMT 2012
Unique Job ID | 73a762ade1748b15

Summary |

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

Model (left) based on template d1utaa_
Top template information
Fold:Ferredoxin-like Superfamily:Sporulation related repeat Family:Sporulation related repeat
Confidence and coverage
Confidence: | 99.9% | Coverage: | 24%
76 residues ( 24% of your sequence) have been modelled with 99.9% 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.
Warning: 71% of your sequence is predicted disordered. Disordered regions cannot be meaningfully predicted.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | A | Q | R | D | Y | V | R | R | S | Q | P | A | P | S | R | R | K | K | S | T | S | R | K | K | Q | R | N | L | P | A | V | S | P | A | M | V | A | I | A | A | A | V | L | V | T | F | I | G | G | L | Y | F | I | T | H | H | K | K | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | E | S | E | T | L | Q | S | Q | K | V | T | G | N | G | L | P | P | K | P | E | E | R | W | R | Y | I | K | E | L | E | S | R | Q | P | G | V | R | A | P | T | E | P | S | A | G | G | E | V | K | T | P | E | Q | L | T | P | E | Q | R | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | L | L | E | Q | M | Q | A | D | M | R | Q | Q | P | T | Q | L | V | E | V | P | W | N | E | Q | T | P | E | Q | R | Q | Q | T | L | Q | R | Q | R | Q | A | Q | Q | L | A | E | Q | Q | R | L | A | Q | Q | S | R | T | T | E | Q | S | W | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | Q | Q | T | R | T | S | Q | A | A | P | V | Q | A | Q | P | R | Q | S | K | P | A | S | S | Q | Q | P | Y | Q | D | L | L | Q | T | P | A | H | T | T | A | Q | S | K | P | Q | Q | A | A | P | V | A | R | A | A | D | A | P | K | P | T | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | E | K | K | D | E | R | R | W | M | V | Q | C | G | S | F | R | G | A | E | Q | A | E | T | V | R | A | Q | L | A | F | E | G | F | D | S | K | I | T | T | N | N | G | W | N | R | V | V | I | G | P | V | K | G | K | E | N | A | D | S | T
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | .
Sequence |  | L | N | R | L | K | M | A | G | H | T | N | C | I | R | L | A | A | G | 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 |
| d1utaa_ |

### PDB 1uta chain A

Region: 244 - 319
Aligned: 76
Modelled: 76
Confidence: 99.9%
Identity: 100%
Fold: Ferredoxin-like
Superfamily: Sporulation related repeat
Family: Sporulation related repeat

Phyre2
2 |
| c1x60A_ |

### PDB 1x60 chain A

Region: 240 - 315
Aligned: 76
Modelled: 76
Confidence: 99.8%
Identity: 29%
PDB header:hydrolase
Chain: A: PDB Molecule:sporulation-specific n-acetylmuramoyl-l-alanine
PDBTitle: solution structure of the peptidoglycan binding domain of2 b. subtilis cell wall lytic enzyme cwlc

Phyre2
3 |
| c3caiA_ |

### PDB 3cai chain A

Region: 260 - 308
Aligned: 49
Modelled: 49
Confidence: 88.0%
Identity: 22%
PDB header:transferase
Chain: A: PDB Molecule:possible aminotransferase;
PDBTitle: crystal structure of mycobacterium tuberculosis rv3778c2 protein

Phyre2
4 |
| d1bs0a_ |

### PDB 1bs0 chain A

Region: 255 - 308
Aligned: 54
Modelled: 54
Confidence: 87.6%
Identity: 17%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: GABA-aminotransferase-like

Phyre2
5 |
| d1elua_ |

### PDB 1elu chain A

Region: 255 - 308
Aligned: 54
Modelled: 54
Confidence: 85.5%
Identity: 13%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: Cystathionine synthase-like

Phyre2
6 |
| c3f9tB_ |

### PDB 3f9t chain B

Region: 260 - 306
Aligned: 47
Modelled: 47
Confidence: 81.6%
Identity: 19%
PDB header:lyase
Chain: B: PDB Molecule:l-tyrosine decarboxylase mfna;
PDBTitle: crystal structure of l-tyrosine decarboxylase mfna (ec 4.1.1.25)2 (np_247014.1) from methanococcus jannaschii at 2.11 a resolution

Phyre2
7 |
| d1t3ia_ |

### PDB 1t3i chain A

Region: 260 - 307
Aligned: 48
Modelled: 48
Confidence: 65.9%
Identity: 23%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: Cystathionine synthase-like

Phyre2
8 |
| c2k49A_ |

### PDB 2k49 chain A

Region: 243 - 314
Aligned: 72
Modelled: 72
Confidence: 59.9%
Identity: 10%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0339 protein so_3888;
PDBTitle: solution nmr structure of upf0339 protein so3888 from shewanella2 oneidensis. northeast structural genomics consortium target sor190

Phyre2
9 |
| d1iuga_ |

### PDB 1iug chain A

Region: 255 - 306
Aligned: 52
Modelled: 52
Confidence: 59.2%
Identity: 10%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: Cystathionine synthase-like

Phyre2
10 |
| c3hdoB_ |

### PDB 3hdo chain B

Region: 261 - 308
Aligned: 45
Modelled: 48
Confidence: 59.1%
Identity: 24%
PDB header:transferase
Chain: B: PDB Molecule:histidinol-phosphate aminotransferase;
PDBTitle: crystal structure of a histidinol-phosphate aminotransferase from2 geobacter metallireducens

Phyre2
11 |
| c3cq6E_ |

### PDB 3cq6 chain E

Region: 255 - 306
Aligned: 49
Modelled: 52
Confidence: 58.3%
Identity: 18%
PDB header:transferase
Chain: E: PDB Molecule:histidinol-phosphate aminotransferase;
PDBTitle: histidinol-phosphate aminotransferase from corynebacterium2 glutamicum holo-form (plp covalently bound )

Phyre2
12 |
| d1m32a_ |

### PDB 1m32 chain A

Region: 261 - 307
Aligned: 47
Modelled: 47
Confidence: 58.0%
Identity: 13%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: Cystathionine synthase-like

Phyre2
13 |
| c2fyfB_ |

### PDB 2fyf chain B

Region: 261 - 305
Aligned: 45
Modelled: 45
Confidence: 56.4%
Identity: 18%
PDB header:transferase
Chain: B: PDB Molecule:phosphoserine aminotransferase;
PDBTitle: structure of a putative phosphoserine aminotransferase from2 mycobacterium tuberculosis

Phyre2
14 |
| c2yrrA_ |

### PDB 2yrr chain A

Region: 255 - 307
Aligned: 53
Modelled: 53
Confidence: 52.9%
Identity: 23%
PDB header:transferase
Chain: A: PDB Molecule:aminotransferase, class v;
PDBTitle: hypothetical alanine aminotransferase (tth0173) from thermus2 thermophilus hb8

Phyre2
15 |
| d1qz9a_ |

### PDB 1qz9 chain A

Region: 260 - 306
Aligned: 46
Modelled: 47
Confidence: 52.8%
Identity: 13%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: Cystathionine synthase-like

Phyre2
16 |
| d1v72a1 |

### PDB 1v72 chain A domain 1

Region: 262 - 307
Aligned: 46
Modelled: 46
Confidence: 52.6%
Identity: 22%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: AAT-like

Phyre2
17 |
| c3hqtB_ |

### PDB 3hqt chain B

Region: 255 - 307
Aligned: 53
Modelled: 53
Confidence: 49.8%
Identity: 19%
PDB header:transferase
Chain: B: PDB Molecule:cai-1 autoinducer synthase;
PDBTitle: plp-dependent acyl-coa transferase cqsa

Phyre2
18 |
| d1wyua1 |

### PDB 1wyu chain A domain 1

Region: 255 - 305
Aligned: 51
Modelled: 51
Confidence: 47.6%
Identity: 20%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: Glycine dehydrogenase subunits (GDC-P)

Phyre2
19 |
| c3rggD_ |

### PDB 3rgg chain D

Region: 249 - 319
Aligned: 63
Modelled: 71
Confidence: 46.5%
Identity: 19%
PDB header:lyase
Chain: D: PDB Molecule:phosphoribosylaminoimidazole carboxylase, pure protein;
PDBTitle: crystal structure of treponema denticola pure bound to air

Phyre2
20 |
| d2f8ja1 |

### PDB 2f8j chain A domain 1

Region: 257 - 306
Aligned: 45
Modelled: 50
Confidence: 46.5%
Identity: 22%
Fold: PLP-dependent transferase-like
Superfamily: PLP-dependent transferases
Family: AAT-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1utaa_ |
|  | 99.9 | 100 | Fold:Ferredoxin-like Superfamily:Sporulation related repeat Family:Sporulation related repeat
2 | c1x60A_ |
|  | 99.8 | 29 | PDB header:hydrolase Chain: A: PDB Molecule:sporulation-specific n-acetylmuramoyl-l-alanine PDBTitle: solution structure of the peptidoglycan binding domain of2 b. subtilis cell wall lytic enzyme cwlc
3 | c3caiA_ |
|  | 88.0 | 22 | PDB header:transferase Chain: A: PDB Molecule:possible aminotransferase; PDBTitle: crystal structure of mycobacterium tuberculosis rv3778c2 protein
4 | d1bs0a_ |
|  | 87.6 | 17 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like
5 | d1elua_ |
|  | 85.5 | 13 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like
6 | c3f9tB_ |
|  | 81.6 | 19 | PDB header:lyase Chain: B: PDB Molecule:l-tyrosine decarboxylase mfna; PDBTitle: crystal structure of l-tyrosine decarboxylase mfna (ec 4.1.1.25)2 (np_247014.1) from methanococcus jannaschii at 2.11 a resolution
7 | d1t3ia_ |
|  | 65.9 | 23 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like
8 | c2k49A_ |
|  | 59.9 | 10 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0339 protein so_3888; PDBTitle: solution nmr structure of upf0339 protein so3888 from shewanella2 oneidensis. northeast structural genomics consortium target sor190
9 | d1iuga_ |
|  | 59.2 | 10 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like
10 | c3hdoB_ |
|  | 59.1 | 24 | PDB header:transferase Chain: B: PDB Molecule:histidinol-phosphate aminotransferase; PDBTitle: crystal structure of a histidinol-phosphate aminotransferase from2 geobacter metallireducens
11 | c3cq6E_ |
|  | 58.3 | 18 | PDB header:transferase Chain: E: PDB Molecule:histidinol-phosphate aminotransferase; PDBTitle: histidinol-phosphate aminotransferase from corynebacterium2 glutamicum holo-form (plp covalently bound )
12 | d1m32a_ |
|  | 58.0 | 13 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like
13 | c2fyfB_ |
|  | 56.4 | 18 | PDB header:transferase Chain: B: PDB Molecule:phosphoserine aminotransferase; PDBTitle: structure of a putative phosphoserine aminotransferase from2 mycobacterium tuberculosis
14 | c2yrrA_ |
|  | 52.9 | 23 | PDB header:transferase Chain: A: PDB Molecule:aminotransferase, class v; PDBTitle: hypothetical alanine aminotransferase (tth0173) from thermus2 thermophilus hb8
15 | d1qz9a_ |
|  | 52.8 | 13 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like
16 | d1v72a1 |
|  | 52.6 | 22 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:AAT-like
17 | c3hqtB_ |
|  | 49.8 | 19 | PDB header:transferase Chain: B: PDB Molecule:cai-1 autoinducer synthase; PDBTitle: plp-dependent acyl-coa transferase cqsa
18 | d1wyua1 |
|  | 47.6 | 20 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Glycine dehydrogenase subunits (GDC-P)
19 | c3rggD_ |
|  | 46.5 | 19 | PDB header:lyase Chain: D: PDB Molecule:phosphoribosylaminoimidazole carboxylase, pure protein; PDBTitle: crystal structure of treponema denticola pure bound to air
20 | d2f8ja1 |
|  | 46.5 | 22 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:AAT-like
21 | c2k8eA_ |
| not modelled | 46.3 | 11 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0339 protein yegp; PDBTitle: solution nmr structure of protein of unknown function yegp from e.2 coli. ontario center for structural proteomics target ec0640_1_1233 northeast structural genomics consortium target et102.
22 | d1eg5a_ |
| not modelled | 44.5 | 17 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like
23 | c3p3dA_ |
| not modelled | 44.2 | 21 | PDB header:nuclear protein Chain: A: PDB Molecule:nucleoporin 53; PDBTitle: crystal structure of the nup53 rrm domain from pichia guilliermondii
24 | d1gcca_ |
| not modelled | 43.5 | 26 | Fold:DNA-binding domain Superfamily:DNA-binding domain Family:GCC-box binding domain
25 | c2adbA_ |
| not modelled | 43.0 | 9 | PDB header:rna binding protein/rna Chain: A: PDB Molecule:polypyrimidine tract-binding protein 1; PDBTitle: solution structure of polypyrimidine tract binding protein2 rbd2 complexed with cucucu rna
26 | d1dq3a4 |
| not modelled | 41.6 | 14 | Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Intein endonuclease
27 | c2y9jt_ |
| not modelled | 41.0 | 14 | PDB header:protein transport Chain: T: PDB Molecule:protein prgh; PDBTitle: three-dimensional model of salmonella's needle complex at2 subnanometer resolution
28 | d1u11a_ |
| not modelled | 40.0 | 16 | Fold:Flavodoxin-like Superfamily:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
29 | c2w8wA_ |
| not modelled | 39.7 | 19 | PDB header:transferase Chain: A: PDB Molecule:serine palmitoyltransferase; PDBTitle: n100y spt with plp-ser
30 | d2c0ra1 |
| not modelled | 38.5 | 16 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like
31 | c2x7iA_ |
| not modelled | 37.9 | 17 | PDB header:transferase Chain: A: PDB Molecule:mevalonate kinase; PDBTitle: crystal structure of mevalonate kinase from methicillin-2 resistant staphylococcus aureus mrsa252
32 | c3a2bA_ |
| not modelled | 37.6 | 13 | PDB header:transferase Chain: A: PDB Molecule:serine palmitoyltransferase; PDBTitle: crystal structure of serine palmitoyltransferase from sphingobacterium2 multivorum with substrate l-serine
33 | d1ztpa1 |
| not modelled | 36.4 | 8 | Fold:eIF4e-like Superfamily:eIF4e-like Family:BLES03-like
34 | d1nz8a_ |
| not modelled | 35.9 | 17 | Fold:Ferredoxin-like Superfamily:N-utilization substance G protein NusG, N-terminal domain Family:N-utilization substance G protein NusG, N-terminal domain
35 | d1wg1a_ |
| not modelled | 35.7 | 8 | Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD
36 | c2fw9A_ |
| not modelled | 35.2 | 16 | PDB header:lyase Chain: A: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide mutase; PDBTitle: structure of pure (n5-carboxyaminoimidazole ribonucleotide mutase)2 h59f from the acidophilic bacterium acetobacter aceti, at ph 8
37 | d2hk6a1 |
| not modelled | 33.5 | 15 | Fold:Chelatase-like Superfamily:Chelatase Family:Ferrochelatase
38 | d1jf9a_ |
| not modelled | 33.3 | 17 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like
39 | c3f0hA_ |
| not modelled | 33.2 | 13 | PDB header:transferase Chain: A: PDB Molecule:aminotransferase; PDBTitle: crystal structure of aminotransferase (rer070207000802) from2 eubacterium rectale at 1.70 a resolution
40 | c3pn8A_ |
| not modelled | 32.3 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:putative phospho-beta-glucosidase; PDBTitle: the crystal structure of 6-phospho-beta-glucosidase from streptococcus2 mutans ua159
41 | c3lp6D_ |
| not modelled | 32.1 | 21 | PDB header:lyase Chain: D: PDB Molecule:phosphoribosylaminoimidazole carboxylase catalytic subunit; PDBTitle: crystal structure of rv3275c-e60a from mycobacterium tuberculosis at2 1.7a resolution
42 | d1qcza_ |
| not modelled | 31.8 | 16 | Fold:Flavodoxin-like Superfamily:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
43 | c3e9kA_ |
| not modelled | 31.1 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:kynureninase; PDBTitle: crystal structure of homo sapiens kynureninase-3-hydroxyhippuric acid2 inhibitor complex
44 | c3trhI_ |
| not modelled | 30.8 | 16 | PDB header:lyase Chain: I: PDB Molecule:phosphoribosylaminoimidazole carboxylase PDBTitle: structure of a phosphoribosylaminoimidazole carboxylase catalytic2 subunit (pure) from coxiella burnetii
45 | c2dr1A_ |
| not modelled | 29.2 | 11 | PDB header:transferase Chain: A: PDB Molecule:386aa long hypothetical serine aminotransferase; PDBTitle: crystal structure of the ph1308 protein from pyrococcus horikoshii ot3
46 | d1m6sa_ |
| not modelled | 28.6 | 16 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:AAT-like
47 | c1yj7A_ |
| not modelled | 28.6 | 12 | PDB header:protein transport Chain: A: PDB Molecule:escj; PDBTitle: crystal structure of enteropathogenic e.coli (epec) type iii secretion2 system protein escj
48 | d1nh8a2 |
| not modelled | 28.1 | 12 | Fold:Ferredoxin-like Superfamily:GlnB-like Family:ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain
49 | c3rfaA_ |
| not modelled | 27.8 | 17 | PDB header:oxidoreductase Chain: A: PDB Molecule:ribosomal rna large subunit methyltransferase n; PDBTitle: x-ray structure of rlmn from escherichia coli in complex with s-2 adenosylmethionine
50 | c2k06A_ |
| not modelled | 27.5 | 13 | PDB header:transcription Chain: A: PDB Molecule:transcription antitermination protein nusg; PDBTitle: solution structure of the aminoterminal domain of e. coli2 nusg
51 | c3cbfA_ |
| not modelled | 26.8 | 15 | PDB header:transferase Chain: A: PDB Molecule:alpha-aminodipate aminotransferase; PDBTitle: crystal structure of lysn, alpha-aminoadipate2 aminotransferase, from thermus thermophilus hb27
52 | c2j75A_ |
| not modelled | 26.7 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:beta-glucosidase a; PDBTitle: beta-glucosidase from thermotoga maritima in complex with2 noeuromycin
53 | c3hyjD_ |
| not modelled | 26.5 | 22 | PDB header:transcription regulator Chain: D: PDB Molecule:protein duf199/whia; PDBTitle: crystal structure of the n-terminal laglidadg domain of duf199/whia
54 | c3orsD_ |
| not modelled | 26.3 | 17 | PDB header:isomerase,biosynthetic protein Chain: D: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide mutase; PDBTitle: crystal structure of n5-carboxyaminoimidazole ribonucleotide mutase2 from staphylococcus aureus
55 | d1xmpa_ |
| not modelled | 26.2 | 18 | Fold:Flavodoxin-like Superfamily:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
56 | c3nthA_ |
| not modelled | 25.0 | 16 | PDB header:transcription Chain: A: PDB Molecule:maternal protein tudor; PDBTitle: crystal structure of tudor and aubergine [r13(me2s)] complex
57 | c3mafB_ |
| not modelled | 24.1 | 17 | PDB header:lyase Chain: B: PDB Molecule:sphingosine-1-phosphate lyase; PDBTitle: crystal structure of stspl (asymmetric form)
58 | d1js3a_ |
| not modelled | 23.7 | 6 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Pyridoxal-dependent decarboxylase
59 | c2hzpA_ |
| not modelled | 23.7 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:kynureninase; PDBTitle: crystal structure of homo sapiens kynureninase
60 | c2p2uA_ |
| not modelled | 23.6 | 41 | PDB header:dna binding protein Chain: A: PDB Molecule:host-nuclease inhibitor protein gam, putative; PDBTitle: crystal structure of putative host-nuclease inhibitor2 protein gam from desulfovibrio vulgaris
61 | c2h31A_ |
| not modelled | 23.3 | 18 | PDB header:ligase, lyase Chain: A: PDB Molecule:multifunctional protein ade2; PDBTitle: crystal structure of human paics, a bifunctional carboxylase and2 synthetase in purine biosynthesis
62 | c3nohA_ |
| not modelled | 23.1 | 50 | PDB header:peptide binding protein Chain: A: PDB Molecule:putative peptide binding protein; PDBTitle: crystal structure of a putative peptide binding protein (rumgna_00914)2 from ruminococcus gnavus atcc 29149 at 1.60 a resolution
63 | d1u0bb1 |
| not modelled | 22.5 | 16 | Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
64 | c3bfjK_ |
| not modelled | 21.3 | 15 | PDB header:oxidoreductase Chain: K: PDB Molecule:1,3-propanediol oxidoreductase; PDBTitle: crystal structure analysis of 1,3-propanediol oxidoreductase
65 | c2q5cA_ |
| not modelled | 21.1 | 18 | PDB header:transcription Chain: A: PDB Molecule:ntrc family transcriptional regulator; PDBTitle: crystal structure of ntrc family transcriptional regulator from2 clostridium acetobutylicum
66 | d2cpia1 |
| not modelled | 21.0 | 11 | Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD
67 | d1oj4a2 |
| not modelled | 20.4 | 11 | Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE
68 | d1lbqa_ |
| not modelled | 20.1 | 13 | Fold:Chelatase-like Superfamily:Chelatase Family:Ferrochelatase
69 | c2huuA_ |
| not modelled | 20.1 | 13 | PDB header:transferase Chain: A: PDB Molecule:alanine glyoxylate aminotransferase; PDBTitle: crystal structure of aedes aegypti alanine glyoxylate2 aminotransferase in complex with alanine
70 | c3ffrA_ |
| not modelled | 20.0 | 13 | PDB header:transferase Chain: A: PDB Molecule:phosphoserine aminotransferase serc; PDBTitle: crystal structure of a phosphoserine aminotransferase serc (chu_0995)2 from cytophaga hutchinsonii atcc 33406 at 1.75 a resolution
71 | d1rk8a_ |
| not modelled | 19.7 | 11 | Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD
72 | d1fg7a_ |
| not modelled | 19.5 | 17 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:AAT-like
73 | c3ox4D_ |
| not modelled | 19.3 | 19 | PDB header:oxidoreductase Chain: D: PDB Molecule:alcohol dehydrogenase 2; PDBTitle: structures of iron-dependent alcohol dehydrogenase 2 from zymomonas2 mobilis zm4 complexed with nad cofactor
74 | c2eqkA_ |
| not modelled | 19.0 | 43 | PDB header:transcription Chain: A: PDB Molecule:tudor domain-containing protein 4; PDBTitle: solution structure of the tudor domain of tudor domain-2 containing protein 4
75 | d1wsta1 |
| not modelled | 18.9 | 10 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:AAT-like
76 | d2erra1 |
| not modelled | 18.4 | 8 | Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD
77 | c3o6cA_ |
| not modelled | 18.1 | 12 | PDB header:transferase Chain: A: PDB Molecule:pyridoxine 5'-phosphate synthase; PDBTitle: pyridoxal phosphate biosynthetic protein pdxj from campylobacter2 jejuni
78 | c3hyiA_ |
| not modelled | 18.0 | 18 | PDB header:transcription regulator Chain: A: PDB Molecule:protein duf199/whia; PDBTitle: crystal structure of full-length duf199/whia from thermatoga maritima
79 | d1s0aa_ |
| not modelled | 17.9 | 6 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like
80 | c2z1sA_ |
| not modelled | 17.8 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:beta-glucosidase b; PDBTitle: beta-glucosidase b from paenibacillus polymyxa complexed2 with cellotetraose
81 | c2ordA_ |
| not modelled | 17.6 | 15 | PDB header:transferase Chain: A: PDB Molecule:acetylornithine aminotransferase; PDBTitle: crystal structure of acetylornithine aminotransferase (ec 2.6.1.11)2 (acoat) (tm1785) from thermotoga maritima at 1.40 a resolution
82 | d1kvka2 |
| not modelled | 17.1 | 19 | Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Mevalonate kinase
83 | c2hvzA_ |
| not modelled | 16.8 | 7 | PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor, arginine/serine-rich 7; PDBTitle: solution structure of the rrm domain of sr rich factor 9g8
84 | c2i38A_ |
| not modelled | 16.6 | 12 | PDB header:rna binding protein/chimera Chain: A: PDB Molecule:fusion protein consists of immunoglobin g- PDBTitle: solution structure of the rrm of srp20
85 | c2zoxA_ |
| not modelled | 16.1 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:cytosolic beta-glucosidase; PDBTitle: crystal structure of the covalent intermediate of human cytosolic2 beta-glucosidase
86 | c2iruA_ |
| not modelled | 16.0 | 24 | PDB header:transferase Chain: A: PDB Molecule:putative dna ligase-like protein rv0938/mt0965; PDBTitle: crystal structure of the polymerase domain from mycobacterium2 tuberculosis ligase d
87 | c2dclB_ |
| not modelled | 15.9 | 19 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical upf0166 protein ph1503; PDBTitle: structure of ph1503 protein from pyrococcus horikoshii ot3
88 | d1fsha_ |
| not modelled | 15.9 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain
89 | c3md3A_ |
| not modelled | 15.9 | 4 | PDB header:rna binding protein Chain: A: PDB Molecule:nuclear and cytoplasmic polyadenylated rna-binding protein PDBTitle: crystal structure of the first two rrm domains of yeast poly(u)2 binding protein (pub1)
90 | d2p5ia1 |
| not modelled | 15.7 | 27 | Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:LplA-like
91 | c3ml6D_ |
| not modelled | 15.5 | 15 | PDB header:protein transport Chain: D: PDB Molecule:chimeric complex between protein dishevlled2 homolog dvl-2 PDBTitle: a complex between dishevlled2 and clathrin adaptor ap-2
92 | d1pbga_ |
| not modelled | 15.2 | 14 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Family 1 of glycosyl hydrolase
93 | d1o51a_ |
| not modelled | 14.6 | 16 | Fold:Ferredoxin-like Superfamily:GlnB-like Family:DUF190/COG1993
94 | c1v02F_ |
| not modelled | 14.2 | 20 | PDB header:hydrolase Chain: F: PDB Molecule:dhurrinase; PDBTitle: crystal structure of the sorghum bicolor dhurrinase 1
95 | d1v02a_ |
| not modelled | 14.2 | 20 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Family 1 of glycosyl hydrolase
96 | d2a21a1 |
| not modelled | 14.2 | 15 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I DAHP synthetase
97 | d2k7ia1 |
| not modelled | 14.1 | 11 | Fold:YegP-like Superfamily:YegP-like Family:YegP-like
98 | c2k7iB_ |
| not modelled | 14.1 | 11 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:upf0339 protein atu0232; PDBTitle: solution nmr structure of protein atu0232 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att3. ontario center for structural proteomics target atc0223.
99 | d1rv3a_ |
| not modelled | 14.1 | 10 | Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-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