Phyre 2 Results for Q46942

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Email | l.a.kelley@imperial.ac.uk
Description | Q46942
Date | Thu Jan 5 12:36:01 GMT 2012
Unique Job ID | 33218586a8d18a30

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2zxjB_
Top template information
PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein walr; PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus
Confidence and coverage
Confidence: | 99.9% | Coverage: | 36%
98 residues ( 36% 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.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | Y | W | I | I | N | D | N | I | E | F | W | P | E | H | R | K | L | I | S | V | H | N | A | D | L | N | V | V | L | T | T | P | A | S | R | C | L | S | L | L | L | E | A | F | P | D | V | V | A | Q | Q | D | F | F | T | R | V | W | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | E | E | G | M | R | V | P | T | N | T | L | Y | Q | N | I | S | I | I | R | R | G | F | R | A | V | G | D | T | T | H | S | L | I | A | T | V | P | R | R | G | F | K | I | H | N | D | I | N | I | Q | N | H | V | I | N | S | S | T | D | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | H | T | H | N | A | P | P | A | I | K | V | N | A | G | Y | K | E | S | I | G | G | A | K | N | F | N | N | K | I | L | K | H | I | K | S | H | L | I | M | L | S | A | F | V | I | G | A | Y | S | A | Y | W | L | W | N | N | N | Q | P | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | P | F | F | K | D | Y | K | T | V | A | E | I | N | G | C | H | F | N | V | T | E | D | T | I | D | G | L | K | E | F | D | K | Y | K | T | R | I | L | D | S | G | I | N | C | K | K | H | P | W | L | Y | F | P | L | A | K | S | S | P | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | .
Sequence |  | M | I | V | M | A | C | N | K | N | Y | N | Q | H | E | V | A | N | C | L | T | L | S | Y | R | E | V | N | R | D
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 |
| c2zxjB_ |

### PDB 2zxj chain B

Region: 4 - 106
Aligned: 98
Modelled: 100
Confidence: 99.9%
Identity: 15%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein walr;
PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus

Phyre2
2 |
| d1opca_ |

### PDB 1opc chain A

Region: 4 - 106
Aligned: 98
Modelled: 100
Confidence: 99.9%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2
3 |
| c2hwvA_ |

### PDB 2hwv chain A

Region: 4 - 106
Aligned: 98
Modelled: 103
Confidence: 99.9%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:dna-binding response regulator vicr;
PDBTitle: crystal structure of an essential response regulator dna binding2 domain, vicrc in enterococcus faecalis, a member of the yycf3 subfamily.

Phyre2
4 |
| c2pmuD_ |

### PDB 2pmu chain D

Region: 1 - 106
Aligned: 96
Modelled: 102
Confidence: 99.8%
Identity: 19%
PDB header:transcription regulation
Chain: D: PDB Molecule:response regulator phop;
PDBTitle: crystal structure of the dna-binding domain of phop

Phyre2
5 |
| c3q9vB_ |

### PDB 3q9v chain B

Region: 4 - 105
Aligned: 96
Modelled: 99
Confidence: 99.8%
Identity: 17%
PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding response regulator;
PDBTitle: crystal structure of rra c-terminal domain(123-221) from deinococcus2 radiodurans

Phyre2
6 |
| d1p2fa1 |

### PDB 1p2f chain A domain 1

Region: 3 - 105
Aligned: 95
Modelled: 99
Confidence: 99.8%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2
7 |
| d1gxqa_ |

### PDB 1gxq chain A

Region: 4 - 105
Aligned: 96
Modelled: 102
Confidence: 99.8%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2
8 |
| c2jzyA_ |

### PDB 2jzy chain A

Region: 4 - 108
Aligned: 99
Modelled: 102
Confidence: 99.8%
Identity: 19%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein pcor;
PDBTitle: solution structure of c-terminal effector domain of2 putative two-component-system response regulator involved3 in copper resistance from klebsiella pneumoniae

Phyre2
9 |
| c2hqnA_ |

### PDB 2hqn chain A

Region: 4 - 112
Aligned: 103
Modelled: 109
Confidence: 99.8%
Identity: 21%
PDB header:signaling protein
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism

Phyre2
10 |
| c2k4jA_ |

### PDB 2k4j chain A

Region: 7 - 104
Aligned: 93
Modelled: 98
Confidence: 99.8%
Identity: 15%
PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: arsr dna binding domain

Phyre2
11 |
| d1kgsa1 |

### PDB 1kgs chain A domain 1

Region: 4 - 106
Aligned: 92
Modelled: 100
Confidence: 99.8%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2
12 |
| d1ys7a1 |

### PDB 1ys7 chain A domain 1

Region: 4 - 106
Aligned: 94
Modelled: 100
Confidence: 99.8%
Identity: 26%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2
13 |
| c2oqrA_ |

### PDB 2oqr chain A

Region: 3 - 104
Aligned: 97
Modelled: 102
Confidence: 99.7%
Identity: 19%
PDB header:transcription,signaling protein
Chain: A: PDB Molecule:sensory transduction protein regx3;
PDBTitle: the structure of the response regulator regx3 from mycobacterium2 tuberculosis

Phyre2
14 |
| c1ys7B_ |

### PDB 1ys7 chain B

Region: 4 - 106
Aligned: 96
Modelled: 100
Confidence: 99.7%
Identity: 26%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulatory protein prra;
PDBTitle: crystal structure of the response regulator protein prra comlexed with2 mg2+

Phyre2
15 |
| d2ff4a1 |

### PDB 2ff4 chain A domain 1

Region: 24 - 104
Aligned: 80
Modelled: 81
Confidence: 99.6%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2
16 |
| c2hqrA_ |

### PDB 2hqr chain A

Region: 4 - 106
Aligned: 97
Modelled: 103
Confidence: 99.6%
Identity: 23%
PDB header:signaling protein
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism

Phyre2
17 |
| c2gwrA_ |

### PDB 2gwr chain A

Region: 7 - 106
Aligned: 93
Modelled: 97
Confidence: 99.5%
Identity: 18%
PDB header:signaling protein
Chain: A: PDB Molecule:dna-binding response regulator mtra;
PDBTitle: crystal structure of the response regulator protein mtra from2 mycobacterium tuberculosis

Phyre2
18 |
| c1p2fA_ |

### PDB 1p2f chain A

Region: 7 - 105
Aligned: 92
Modelled: 96
Confidence: 99.4%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure analysis of response regulator drrb, a2 thermotoga maritima ompr/phob homolog

Phyre2
19 |
| c3r0jA_ |

### PDB 3r0j chain A

Region: 4 - 106
Aligned: 96
Modelled: 103
Confidence: 99.4%
Identity: 18%
PDB header:dna binding protein
Chain: A: PDB Molecule:possible two component system response transcriptional
PDBTitle: structure of phop from mycobacterium tuberculosis

Phyre2
20 |
| c1kgsA_ |

### PDB 1kgs chain A

Region: 3 - 106
Aligned: 93
Modelled: 101
Confidence: 99.1%
Identity: 17%
PDB header:dna binding protein
Chain: A: PDB Molecule:dna binding response regulator d;
PDBTitle: crystal structure at 1.50 a of an ompr/phob homolog from thermotoga2 maritima

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2zxjB_ |
|  | 99.9 | 15 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein walr; PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus
2 | d1opca_ |
|  | 99.9 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like
3 | c2hwvA_ |
|  | 99.9 | 13 | PDB header:transcription Chain: A: PDB Molecule:dna-binding response regulator vicr; PDBTitle: crystal structure of an essential response regulator dna binding2 domain, vicrc in enterococcus faecalis, a member of the yycf3 subfamily.
4 | c2pmuD_ |
|  | 99.8 | 19 | PDB header:transcription regulation Chain: D: PDB Molecule:response regulator phop; PDBTitle: crystal structure of the dna-binding domain of phop
5 | c3q9vB_ |
|  | 99.8 | 17 | PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding response regulator; PDBTitle: crystal structure of rra c-terminal domain(123-221) from deinococcus2 radiodurans
6 | d1p2fa1 |
|  | 99.8 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like
7 | d1gxqa_ |
|  | 99.8 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like
8 | c2jzyA_ |
|  | 99.8 | 19 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein pcor; PDBTitle: solution structure of c-terminal effector domain of2 putative two-component-system response regulator involved3 in copper resistance from klebsiella pneumoniae
9 | c2hqnA_ |
|  | 99.8 | 21 | PDB header:signaling protein Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism
10 | c2k4jA_ |
|  | 99.8 | 15 | PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: arsr dna binding domain
11 | d1kgsa1 |
|  | 99.8 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like
12 | d1ys7a1 |
|  | 99.8 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like
13 | c2oqrA_ |
|  | 99.7 | 19 | PDB header:transcription,signaling protein Chain: A: PDB Molecule:sensory transduction protein regx3; PDBTitle: the structure of the response regulator regx3 from mycobacterium2 tuberculosis
14 | c1ys7B_ |
|  | 99.7 | 26 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulatory protein prra; PDBTitle: crystal structure of the response regulator protein prra comlexed with2 mg2+
15 | d2ff4a1 |
|  | 99.6 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like
16 | c2hqrA_ |
|  | 99.6 | 23 | PDB header:signaling protein Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism
17 | c2gwrA_ |
|  | 99.5 | 18 | PDB header:signaling protein Chain: A: PDB Molecule:dna-binding response regulator mtra; PDBTitle: crystal structure of the response regulator protein mtra from2 mycobacterium tuberculosis
18 | c1p2fA_ |
|  | 99.4 | 16 | PDB header:transcription Chain: A: PDB Molecule:response regulator; PDBTitle: crystal structure analysis of response regulator drrb, a2 thermotoga maritima ompr/phob homolog
19 | c3r0jA_ |
|  | 99.4 | 18 | PDB header:dna binding protein Chain: A: PDB Molecule:possible two component system response transcriptional PDBTitle: structure of phop from mycobacterium tuberculosis
20 | c1kgsA_ |
|  | 99.1 | 17 | PDB header:dna binding protein Chain: A: PDB Molecule:dna binding response regulator d; PDBTitle: crystal structure at 1.50 a of an ompr/phob homolog from thermotoga2 maritima
21 | c2ff4B_ |
| not modelled | 99.1 | 18 | PDB header:transcription Chain: B: PDB Molecule:probable regulatory protein embr; PDBTitle: mycobacterium tuberculosis embr in complex with low affinity2 phosphopeptide
22 | c3q9sA_ |
| not modelled | 98.7 | 18 | PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding response regulator; PDBTitle: crystal structure of rra(1-215) from deinococcus radiodurans
23 | d1biaa1 |
| not modelled | 96.0 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
24 | c2ewnA_ |
| not modelled | 95.6 | 21 | PDB header:ligase, transcription Chain: A: PDB Molecule:bira bifunctional protein; PDBTitle: ecoli biotin repressor with co-repressor analog
25 | d1j5ya1 |
| not modelled | 91.3 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
26 | d1o57a1 |
| not modelled | 88.9 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:N-terminal domain of Bacillus PurR
27 | c3k69A_ |
| not modelled | 86.6 | 10 | PDB header:transcription Chain: A: PDB Molecule:putative transcription regulator; PDBTitle: crystal structure of a putative transcriptional regulator (lp_0360)2 from lactobacillus plantarum at 1.95 a resolution
28 | c1j5yA_ |
| not modelled | 86.6 | 24 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family; PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution
29 | c2fu4B_ |
| not modelled | 83.5 | 22 | PDB header:dna binding protein Chain: B: PDB Molecule:ferric uptake regulation protein; PDBTitle: crystal structure of the dna binding domain of e.coli fur (ferric2 uptake regulator)
30 | c2w57A_ |
| not modelled | 82.9 | 14 | PDB header:metal transport Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: crystal structure of the vibrio cholerae ferric uptake2 regulator (fur) reveals structural rearrangement of the3 dna-binding domains
31 | c3r0aB_ |
| not modelled | 82.8 | 9 | PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
32 | c3klnC_ |
| not modelled | 82.6 | 16 | PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst
33 | d1mzba_ |
| not modelled | 82.0 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FUR-like
34 | c2fe3B_ |
| not modelled | 75.4 | 18 | PDB header:dna binding protein Chain: B: PDB Molecule:peroxide operon regulator; PDBTitle: the crystal structure of bacillus subtilis perr-zn reveals a novel2 zn(cys)4 structural redox switch
35 | c2xigA_ |
| not modelled | 71.6 | 6 | PDB header:transcription Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: the structure of the helicobacter pylori ferric uptake2 regulator fur reveals three functional metal binding sites
36 | c3mwmA_ |
| not modelled | 70.7 | 17 | PDB header:transcription Chain: A: PDB Molecule:putative metal uptake regulation protein; PDBTitle: graded expression of zinc-responsive genes through two regulatory2 zinc-binding sites in zur
37 | d1ylfa1 |
| not modelled | 70.0 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator Rrf2
38 | c2o03A_ |
| not modelled | 69.3 | 17 | PDB header:gene regulation Chain: A: PDB Molecule:probable zinc uptake regulation protein furb; PDBTitle: crystal structure of furb from m. tuberculosis- a zinc uptake2 regulator
39 | c3qp5C_ |
| not modelled | 67.6 | 9 | PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
40 | c3sqnB_ |
| not modelled | 63.5 | 21 | PDB header:transcription regulator Chain: B: PDB Molecule:conserved domain protein; PDBTitle: putative mga family transcriptional regulator from enterococcus2 faecalis
41 | c2q0oA_ |
| not modelled | 58.7 | 14 | PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
42 | c1p4xA_ |
| not modelled | 56.3 | 9 | PDB header:transcription Chain: A: PDB Molecule:staphylococcal accessory regulator a homologue; PDBTitle: crystal structure of sars protein from staphylococcus aureus
43 | c1h0mD_ |
| not modelled | 54.9 | 14 | 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
44 | c3by6C_ |
| not modelled | 54.5 | 15 | PDB header:transcription regulator Chain: C: PDB Molecule:predicted transcriptional regulator; PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
45 | c3sztB_ |
| not modelled | 54.4 | 14 | 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
46 | d1l3la1 |
| not modelled | 53.9 | 14 | 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)
47 | c1zn2A_ |
| not modelled | 51.9 | 18 | PDB header:transcription regulator Chain: A: PDB Molecule:response regulatory protein; PDBTitle: low resolution structure of response regulator styr
48 | c2is9A_ |
| not modelled | 51.3 | 20 | PDB header:transcription Chain: A: PDB Molecule:defective in cullin neddylation protein 1; PDBTitle: structure of yeast dcn-1
49 | d1hw1a1 |
| not modelled | 51.1 | 4 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
50 | d1okra_ |
| not modelled | 49.1 | 4 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Penicillinase repressor
51 | c3kevA_ |
| not modelled | 48.2 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:galieria sulfuraria dcun1 domain-containing protein; PDBTitle: x-ray crystal structure of a dcun1 domain-containing protein from2 galdieria sulfuraria
52 | c3c3wB_ |
| not modelled | 48.2 | 20 | PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
53 | c3c7jA_ |
| not modelled | 47.0 | 13 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: crystal structure of transcriptional regulator (gntr family member)2 from pseudomonas syringae pv. tomato str. dc3000
54 | c1o57A_ |
| not modelled | 46.2 | 19 | PDB header:dna binding protein Chain: A: PDB Molecule:pur operon repressor; PDBTitle: crystal structure of the purine operon repressor of2 bacillus subtilis
55 | c3neuA_ |
| not modelled | 45.0 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin1836 protein; PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
56 | c3eyyA_ |
| not modelled | 45.0 | 14 | PDB header:transport Chain: A: PDB Molecule:putative iron uptake regulatory protein; PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition
57 | c1rnlA_ |
| not modelled | 44.9 | 14 | PDB header:signal transduction protein Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl; PDBTitle: the nitrate/nitrite response regulator protein narl from narl
58 | d1hsja1 |
| not modelled | 44.8 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
59 | c3ecoB_ |
| not modelled | 44.6 | 17 | PDB header:transcription Chain: B: PDB Molecule:mepr; PDBTitle: crystal structure of mepr, a transcription regulator of the2 staphylococcus aureus multidrug efflux pump mepa
60 | d1a04a1 |
| not modelled | 43.8 | 14 | 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)
61 | d3broa1 |
| not modelled | 43.5 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
62 | d1p4xa2 |
| not modelled | 43.2 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
63 | c3bwgA_ |
| not modelled | 40.4 | 13 | PDB header:transcription regulator Chain: A: PDB Molecule:uncharacterized hth-type transcriptional regulator yydk; PDBTitle: the crystal structure of possible transcriptional regulator yydk from2 bacillus subtilis subsp. subtilis str. 168
64 | d3bwga1 |
| not modelled | 40.3 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
65 | c3ihuA_ |
| not modelled | 38.7 | 13 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: crystal structure of dna binding protein (yp_298823.1) from ralstonia2 eutropha jmp134 at 1.92 a resolution
66 | d2hs5a1 |
| not modelled | 38.5 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
67 | c3edpB_ |
| not modelled | 38.3 | 17 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:lin2111 protein; PDBTitle: the crystal structure of the protein lin2111 (functionally unknown)2 from listeria innocua clip11262
68 | d2frha1 |
| not modelled | 38.0 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
69 | c1zljE_ |
| not modelled | 35.7 | 20 | PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
70 | d2d1ha1 |
| not modelled | 35.6 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
71 | d1yioa1 |
| not modelled | 34.8 | 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)
72 | d1fsea_ |
| not modelled | 33.8 | 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)
73 | c2y75F_ |
| not modelled | 33.8 | 12 | PDB header:transcription Chain: F: PDB Molecule:hth-type transcriptional regulator cymr; PDBTitle: the structure of cymr (yrzc) the global cysteine regulator2 of b. subtilis
74 | d1p4xa1 |
| not modelled | 33.6 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
75 | d1p4wa_ |
| not modelled | 33.4 | 14 | 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)
76 | d1stza1 |
| not modelled | 33.0 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain
77 | c2di3A_ |
| not modelled | 32.0 | 17 | PDB header:transcription Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family; PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum
78 | c3ic7A_ |
| not modelled | 29.4 | 14 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator of gntr family2 from bacteroides thetaiotaomicron
79 | c1e2xA_ |
| not modelled | 29.3 | 6 | PDB header:transcriptional regulation Chain: A: PDB Molecule:fatty acid metabolism regulator protein; PDBTitle: fadr, fatty acid responsive transcription factor from e.2 coli
80 | c2rnjA_ |
| not modelled | 29.3 | 18 | PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain
81 | c1x3uA_ |
| not modelled | 24.1 | 11 | 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
82 | c2k4bA_ |
| not modelled | 22.3 | 4 | PDB header:dna binding protein Chain: A: PDB Molecule:transcriptional regulator; PDBTitle: copr repressor structure
83 | c3ctzA_ |
| not modelled | 22.3 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:xaa-pro aminopeptidase 1; PDBTitle: structure of human cytosolic x-prolyl aminopeptidase
84 | d1v4ra1 |
| not modelled | 21.6 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
85 | c2wv0H_ |
| not modelled | 21.3 | 4 | PDB header:transcription Chain: H: PDB Molecule:hth-type transcriptional repressor yvoa; PDBTitle: crystal structure of the gntr-hutc family member yvoa from2 bacillus subtilis
86 | c3cloC_ |
| not modelled | 21.1 | 11 | 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
87 | d1sfxa_ |
| not modelled | 21.0 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
88 | c2hs5A_ |
| not modelled | 20.3 | 15 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcriptional regulator gntr; PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator gntr from rhodococcus sp. rha1
89 | c2krfB_ |
| not modelled | 19.5 | 12 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
90 | d1b4aa1 |
| not modelled | 19.5 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
91 | c3bddD_ |
| not modelled | 19.3 | 14 | PDB header:transcription Chain: D: PDB Molecule:regulatory protein marr; PDBTitle: crystal structure of a putative multiple antibiotic-resistance2 repressor (ssu05_1136) from streptococcus suis 89/1591 at 2.20 a3 resolution
92 | c3fmsA_ |
| not modelled | 19.0 | 20 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: crystal structure of tm0439, a gntr transcriptional2 regulator
93 | d2p5ka1 |
| not modelled | 18.8 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
94 | c2wteB_ |
| not modelled | 18.1 | 14 | PDB header:antiviral protein Chain: B: PDB Molecule:csa3; PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution.
95 | c3lwfD_ |
| not modelled | 18.1 | 12 | PDB header:transcription regulator Chain: D: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator (np_470886.1)2 from listeria innocua at 2.06 a resolution
96 | c3nqoB_ |
| not modelled | 18.1 | 9 | PDB header:transcription Chain: B: PDB Molecule:marr-family transcriptional regulator; PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
97 | c3ketA_ |
| not modelled | 18.0 | 14 | PDB header:transcription/dna Chain: A: PDB Molecule:redox-sensing transcriptional repressor rex; PDBTitle: crystal structure of a rex-family transcriptional regulatory protein2 from streptococcus agalactiae bound to a palindromic operator
98 | d1lj9a_ |
| not modelled | 16.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
99 | c2nnnB_ |
| not modelled | 16.6 | 19 | PDB header:transcription Chain: B: PDB Molecule:probable transcriptional regulator; PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa

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