Phyre 2 Results for P77607

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Email | l.a.kelley@imperial.ac.uk
Description | P77607
Date | Thu Jan 5 12:30:58 GMT 2012
Unique Job ID | 1d3a40cb7c11de8a

Summary |

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

Model (left) based on template c2gm4B_
Top template information
PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna
Confidence and coverage
Confidence: | 100.0% | Coverage: | 74%
172 residues ( 74% 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 | R | G | K | I | L | L | Y | Q | L | K | Y | R | W | Q | S | L | S | I | F | G | C | F | L | C | K | M | T | L | F | R | Y | Q | K | I | I | Y | D | T | G | V | H | Q | M | R | S | F | F | Y | T | I | C | S | S | E | Q | Q | E | S | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | T | D | H | H | S | L | A | E | I | C | Q | K | F | N | I | L | P | E | H | V | V | I | E | Q | V | D | I | K | E | V | V | S | E | Q | R | L | L | R | Q | L | I | H | H | E | M | N | R | Q | D | T | L | V | I | P | D | L | S | C | L | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | R | T | V | E | D | L | Q | N | I | L | F | F | C | L | Q | K | E | M | F | I | Y | S | Y | H | P | A | S | R | I | E | P | S | A | E | S | C | L | S | F | L | I | A | R | Q | D | T | I | D | I | H | N | L | K | S | T | K | S | R | Y | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | .
Sequence |  | H | V | K | K | K | L | G | R | K | E | G | S | K | Y | R | R | D | I | T | I | L | K | K | G | G | F | T | Q | A | E | I | A | K | K | L | S | I | S | L | S | T | V | K | R | H | W | N | N | G | I | I | 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 |
| c2gm4B_ |

### PDB 2gm4 chain B

Region: 46 - 229
Aligned: 172
Modelled: 184
Confidence: 100.0%
Identity: 16%
PDB header:recombination, dna
Chain: B: PDB Molecule:transposon gamma-delta resolvase;
PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna

Phyre2
2 |
| c2r0qF_ |

### PDB 2r0q chain F

Region: 44 - 230
Aligned: 171
Modelled: 180
Confidence: 100.0%
Identity: 17%
PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex

Phyre2
3 |
| d1gdta2 |

### PDB 1gdt chain A domain 2

Region: 44 - 186
Aligned: 136
Modelled: 143
Confidence: 99.9%
Identity: 15%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2
4 |
| d2gm4a2 |

### PDB 2gm4 chain A domain 2

Region: 44 - 186
Aligned: 132
Modelled: 139
Confidence: 99.9%
Identity: 13%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2
5 |
| c3g13B_ |

### PDB 3g13 chain B

Region: 41 - 170
Aligned: 129
Modelled: 130
Confidence: 99.9%
Identity: 9%
PDB header:recombination
Chain: B: PDB Molecule:putative conjugative transposon recombinase;
PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile

Phyre2
6 |
| c3pkzK_ |

### PDB 3pkz chain K

Region: 44 - 168
Aligned: 116
Modelled: 118
Confidence: 99.8%
Identity: 16%
PDB header:recombination
Chain: K: PDB Molecule:recombinase sin;
PDBTitle: structural basis for catalytic activation of a serine recombinase

Phyre2
7 |
| d2rsla_ |

### PDB 2rsl chain A

Region: 44 - 171
Aligned: 114
Modelled: 115
Confidence: 99.8%
Identity: 16%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2
8 |
| c3guvA_ |

### PDB 3guv chain A

Region: 43 - 182
Aligned: 138
Modelled: 140
Confidence: 99.8%
Identity: 10%
PDB header:recombination
Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein;
PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae

Phyre2
9 |
| c3ploX_ |

### PDB 3plo chain X

Region: 46 - 174
Aligned: 120
Modelled: 127
Confidence: 99.8%
Identity: 13%
PDB header:recombination
Chain: X: PDB Molecule:dna-invertase;
PDBTitle: crystal structure of the fis-independent mutant of gin

Phyre2
10 |
| c3bvpB_ |

### PDB 3bvp chain B

Region: 45 - 170
Aligned: 123
Modelled: 126
Confidence: 99.8%
Identity: 14%
PDB header:recombination
Chain: B: PDB Molecule:tp901-1 integrase;
PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase

Phyre2
11 |
| d1hx7a_ |

### PDB 1hx7 chain A

Region: 44 - 155
Aligned: 105
Modelled: 112
Confidence: 99.8%
Identity: 17%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2
12 |
| c3lhfC_ |

### PDB 3lhf chain C

Region: 45 - 180
Aligned: 127
Modelled: 136
Confidence: 99.7%
Identity: 14%
PDB header:recombination
Chain: C: PDB Molecule:serine recombinase;
PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a

Phyre2
13 |
| c3lhkA_ |

### PDB 3lhk chain A

Region: 45 - 184
Aligned: 132
Modelled: 140
Confidence: 99.7%
Identity: 11%
PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna binding protein mj0014;
PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii.

Phyre2
14 |
| d1ijwc_ |

### PDB 1ijw chain C

Region: 187 - 231
Aligned: 45
Modelled: 45
Confidence: 97.4%
Identity: 24%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Recombinase DNA-binding domain

Phyre2
15 |
| d1hcra_ |

### PDB 1hcr chain A

Region: 187 - 231
Aligned: 45
Modelled: 45
Confidence: 97.3%
Identity: 24%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Recombinase DNA-binding domain

Phyre2
16 |
| c1u78A_ |

### PDB 1u78 chain A

Region: 185 - 228
Aligned: 44
Modelled: 44
Confidence: 97.0%
Identity: 16%
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna

Phyre2
17 |
| d1pdnc_ |

### PDB 1pdn chain C

Region: 187 - 228
Aligned: 42
Modelled: 42
Confidence: 96.7%
Identity: 24%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2
18 |
| c6paxA_ |

### PDB 6pax chain A

Region: 187 - 228
Aligned: 42
Modelled: 42
Confidence: 96.6%
Identity: 24%
PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeobox protein pax-6;
PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions

Phyre2
19 |
| d1k78a1 |

### PDB 1k78 chain A domain 1

Region: 187 - 224
Aligned: 38
Modelled: 38
Confidence: 96.3%
Identity: 26%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2
20 |
| c3o60A_ |

### PDB 3o60 chain A

Region: 195 - 228
Aligned: 34
Modelled: 34
Confidence: 96.2%
Identity: 12%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin0861 protein;
PDBTitle: the crystal structure of lin0861 from listeria innocua to 2.8a

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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2gm4B_ |
|  | 100.0 | 16 | PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna
2 | c2r0qF_ |
|  | 100.0 | 17 | PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
3 | d1gdta2 |
|  | 99.9 | 15 | Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain
4 | d2gm4a2 |
|  | 99.9 | 13 | Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain
5 | c3g13B_ |
|  | 99.9 | 9 | PDB header:recombination Chain: B: PDB Molecule:putative conjugative transposon recombinase; PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile
6 | c3pkzK_ |
|  | 99.8 | 16 | PDB header:recombination Chain: K: PDB Molecule:recombinase sin; PDBTitle: structural basis for catalytic activation of a serine recombinase
7 | d2rsla_ |
|  | 99.8 | 16 | Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain
8 | c3guvA_ |
|  | 99.8 | 10 | PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein; PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae
9 | c3ploX_ |
|  | 99.8 | 13 | PDB header:recombination Chain: X: PDB Molecule:dna-invertase; PDBTitle: crystal structure of the fis-independent mutant of gin
10 | c3bvpB_ |
|  | 99.8 | 14 | PDB header:recombination Chain: B: PDB Molecule:tp901-1 integrase; PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase
11 | d1hx7a_ |
|  | 99.8 | 17 | Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain
12 | c3lhfC_ |
|  | 99.7 | 14 | PDB header:recombination Chain: C: PDB Molecule:serine recombinase; PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a
13 | c3lhkA_ |
|  | 99.7 | 11 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna binding protein mj0014; PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii.
14 | d1ijwc_ |
|  | 97.4 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain
15 | d1hcra_ |
|  | 97.3 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain
16 | c1u78A_ |
|  | 97.0 | 16 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
17 | d1pdnc_ |
|  | 96.7 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
18 | c6paxA_ |
|  | 96.6 | 24 | PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions
19 | d1k78a1 |
|  | 96.3 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
20 | c3o60A_ |
|  | 96.2 | 12 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin0861 protein; PDBTitle: the crystal structure of lin0861 from listeria innocua to 2.8a
21 | d2g7la1 |
| not modelled | 96.2 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
22 | c3ljlB_ |
| not modelled | 96.0 | 12 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator luxt; PDBTitle: the crystal structure of the full-length transcriptional regulator2 luxt from vibrio parahaemolyticus rimd 2210633.
23 | d2fq4a1 |
| not modelled | 95.9 | 28 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
24 | c3sztB_ |
| not modelled | 95.8 | 18 | PDB header:transcription Chain: B: PDB Molecule:quorum-sensing control repressor; PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone
25 | d2gena1 |
| not modelled | 95.7 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
26 | d6paxa1 |
| not modelled | 95.7 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
27 | d1zk8a1 |
| not modelled | 95.7 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
28 | d1jt6a1 |
| not modelled | 95.7 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
29 | d1t56a1 |
| not modelled | 95.6 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
30 | d2hyja1 |
| not modelled | 95.6 | 32 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
31 | d1vi0a1 |
| not modelled | 95.6 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
32 | d1rkta1 |
| not modelled | 95.6 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
33 | d1ui5a1 |
| not modelled | 95.6 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
34 | d2vkva1 |
| not modelled | 95.6 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
35 | d1v7ba1 |
| not modelled | 95.5 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
36 | d2iu5a1 |
| not modelled | 95.5 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
37 | c3mvpA_ |
| not modelled | 95.5 | 32 | PDB header:transcription regulator Chain: A: PDB Molecule:tetr/acrr transcriptional regulator; PDBTitle: the crystal structure of a tetr/acrr transcriptional regulator from2 streptococcus mutans to 1.85a
38 | c2iaiA_ |
| not modelled | 95.5 | 24 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative transcriptional regulator sco3833; PDBTitle: crystal structure of sco3833, a member of the tetr transcriptional2 regulator family from streptomyces coelicolor a3
39 | d2vkea1 |
| not modelled | 95.5 | 32 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
40 | d2gfna1 |
| not modelled | 95.5 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
41 | d2o7ta1 |
| not modelled | 95.4 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
42 | c2pbxB_ |
| not modelled | 95.4 | 28 | PDB header:transcription Chain: B: PDB Molecule:hemagglutinin/protease regulatory protein; PDBTitle: vibrio cholerae hapr
43 | d2id6a1 |
| not modelled | 95.4 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
44 | d2id3a1 |
| not modelled | 95.3 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
45 | d2oi8a1 |
| not modelled | 95.3 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
46 | d2fd5a1 |
| not modelled | 95.3 | 8 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
47 | d2fbqa1 |
| not modelled | 95.3 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
48 | d2d6ya1 |
| not modelled | 95.2 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
49 | d2fx0a1 |
| not modelled | 95.2 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
50 | c3e7qB_ |
| not modelled | 95.2 | 17 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: the crystal structure of the putative transcriptional regulator from2 pseudomonas aeruginosa pao1
51 | c3g7rB_ |
| not modelled | 95.2 | 16 | PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of sco4454, a tetr-family transcriptional2 regulator from streptomyces coelicolor
52 | c3kkcB_ |
| not modelled | 95.2 | 16 | PDB header:transcription regulator Chain: B: PDB Molecule:tetr family transcriptional regulator; PDBTitle: the crystal structure of tetr transcriptional regulator from2 streptococcus agalactiae 2603v
53 | d2g7ga1 |
| not modelled | 95.2 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
54 | d3c07a1 |
| not modelled | 95.2 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
55 | c2elhA_ |
| not modelled | 95.2 | 17 | PDB header:dna binding protein Chain: A: PDB Molecule:cg11849-pa; PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa
56 | d2i10a1 |
| not modelled | 95.1 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
57 | d2np5a1 |
| not modelled | 95.1 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
58 | d1pb6a1 |
| not modelled | 95.1 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
59 | d2g7sa1 |
| not modelled | 95.1 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
60 | c2y31A_ |
| not modelled | 95.0 | 8 | PDB header:transcription Chain: A: PDB Molecule:putative repressor simreg2; PDBTitle: simocyclinone c4 bound form of tetr-like repressor simr
61 | d2g3ba1 |
| not modelled | 95.0 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
62 | d2coba1 |
| not modelled | 95.0 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain
63 | c3nrgA_ |
| not modelled | 94.9 | 8 | PDB header:transcription Chain: A: PDB Molecule:tetr family transcriptional regulator; PDBTitle: crystal structure of a tetr family transcriptional regulator2 (caur_2714) from chloroflexus aurantiacus j-10-fl at 2.56 a3 resolution
64 | d1sgma1 |
| not modelled | 94.9 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
65 | c2k27A_ |
| not modelled | 94.9 | 24 | PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain
66 | d1nera_ |
| not modelled | 94.9 | 12 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
67 | d1gdta1 |
| not modelled | 94.8 | 29 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain
68 | d1z0xa1 |
| not modelled | 94.7 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
69 | d1fsea_ |
| not modelled | 94.6 | 34 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
70 | d1a04a1 |
| not modelled | 94.6 | 38 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
71 | c2q0oA_ |
| not modelled | 94.5 | 19 | PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
72 | c1h0mD_ |
| not modelled | 94.4 | 15 | PDB header:transcription/dna Chain: D: PDB Molecule:transcriptional activator protein trar; PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna
73 | c1zljE_ |
| not modelled | 94.4 | 24 | PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
74 | d2hkua1 |
| not modelled | 94.3 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
75 | c1r71B_ |
| not modelled | 94.1 | 22 | PDB header:transcription/dna Chain: B: PDB Molecule:transcriptional repressor protein korb; PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna
76 | c3b7hA_ |
| not modelled | 94.1 | 14 | PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11
77 | c3qp5C_ |
| not modelled | 94.0 | 43 | PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
78 | c1x3uA_ |
| not modelled | 94.0 | 32 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
79 | c3frwF_ |
| not modelled | 94.0 | 23 | PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
80 | c3t76A_ |
| not modelled | 94.0 | 20 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii
81 | d1t33a1 |
| not modelled | 93.9 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
82 | d1biaa1 |
| not modelled | 93.9 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
83 | d1p4wa_ |
| not modelled | 93.9 | 32 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
84 | d1r71a_ |
| not modelled | 93.9 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like
85 | c2jpcA_ |
| not modelled | 93.8 | 38 | PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein
86 | c2krfB_ |
| not modelled | 93.8 | 24 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
87 | d1yioa1 |
| not modelled | 93.8 | 29 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
88 | d1l3la1 |
| not modelled | 93.8 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
89 | d2jn6a1 |
| not modelled | 93.7 | 27 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like
90 | c2rnjA_ |
| not modelled | 93.7 | 32 | PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain
91 | d1xsva_ |
| not modelled | 93.7 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
92 | c3c3wB_ |
| not modelled | 93.6 | 18 | PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
93 | d2cg4a1 |
| not modelled | 93.6 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
94 | d2bjca1 |
| not modelled | 93.6 | 27 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
95 | c3mzyA_ |
| not modelled | 93.6 | 24 | PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a
96 | d1trra_ |
| not modelled | 93.5 | 28 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
97 | d1jhga_ |
| not modelled | 93.4 | 31 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
98 | c2l8nA_ |
| not modelled | 93.4 | 35 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional repressor cytr; PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna
99 | c3korD_ |
| not modelled | 93.3 | 29 | PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
100 | d1b0na2 |
| not modelled | 93.3 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
101 | c3bs3A_ |
| not modelled | 93.2 | 23 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of a putative dna-binding protein from bacteroides2 fragilis
102 | d1lcda_ |
| not modelled | 93.2 | 28 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
103 | c2lcvA_ |
| not modelled | 93.0 | 35 | PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional repressor cytr; PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation
104 | d1s7oa_ |
| not modelled | 92.9 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
105 | d1rp3a2 |
| not modelled | 92.9 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
106 | c3trbA_ |
| not modelled | 92.9 | 16 | PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii
107 | d1i1ga1 |
| not modelled | 92.9 | 32 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
108 | d1vz0a1 |
| not modelled | 92.8 | 32 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like
109 | d1hlva1 |
| not modelled | 92.8 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
110 | c2kpjA_ |
| not modelled | 92.8 | 26 | PDB header:transcription regulator Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa; PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a
111 | d1uxda_ |
| not modelled | 92.7 | 26 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
112 | c3cloC_ |
| not modelled | 92.7 | 38 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution
113 | d1y9qa1 |
| not modelled | 92.7 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain
114 | c2ebyA_ |
| not modelled | 92.6 | 24 | PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli
115 | c3hosA_ |
| not modelled | 92.6 | 14 | PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
116 | d1qpza1 |
| not modelled | 92.6 | 32 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
117 | c3hugA_ |
| not modelled | 92.5 | 30 | PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
118 | d1efaa1 |
| not modelled | 92.4 | 27 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
119 | d1j5ya1 |
| not modelled | 92.3 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
120 | c3fmyA_ |
| not modelled | 92.2 | 20 | PDB header:dna binding protein Chain: A: PDB Molecule:hth-type transcriptional regulator mqsa PDBTitle: structure of the c-terminal domain of the e. coli protein2 mqsa (ygit/b3021)

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