Phyre 2 Results for P31062

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P31062
Date | Thu Jan 5 11:46:59 GMT 2012
Unique Job ID | fe19f50d71ff2b31

Summary |

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

Model (left) based on template d1j9ia_
Top template information
Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Terminase gpNU1 subunit domain
Confidence and coverage
Confidence: | 99.5% | Coverage: | 38%
68 residues ( 38% of your sequence) have been modelled with 99.5% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
147 residues ( 81%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | E | V | N | K | K | Q | L | A | D | I | F | G | A | S | I | R | T | I | Q | N | W | Q | E | Q | G | M | P | V | L | R | G | G | G | K | G | N | E | V | L | Y | D | S | A | A | V | I | K | W | Y | A | E | R | D | A | E | I | E | N | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | K | L | R | R | E | V | E | E | L | L | Q | A | S | E | T | D | L | Q | P | G | T | I | E | Y | E | R | H | R | L | T | R | A | Q | A | D | A | Q | E | L | K | N | A | R | D | S | A | E | V | V | E | T | A | F | C | T | F | V | L | S | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | I | A | G | E | I | A | S | I | L | D | G | I | P | L | S | V | Q | R | R | F | P | E | L | E | N | R | H | V | D | F | L | K | R | D | I | I | K | A | M | N | K | A | A | A | L | D | E | L | I | P | G | L | L | S | E | Y | I | E | Q | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  | ? | ? |  |  |  |  |  |  |  |  | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | .
Sequence |  | 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 |
| d1j9ia_ |

### PDB 1j9i chain A

Region: 1 - 68
Aligned: 68
Modelled: 68
Confidence: 99.5%
Identity: 100%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: Terminase gpNU1 subunit domain

Phyre2
2 |
| c3hh0C_ |

### PDB 3hh0 chain C

Region: 1 - 179
Aligned: 125
Modelled: 125
Confidence: 97.1%
Identity: 12%
PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus

Phyre2
3 |
| d1r8da_ |

### PDB 1r8d chain A

Region: 1 - 48
Aligned: 48
Modelled: 48
Confidence: 96.9%
Identity: 27%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2
4 |
| d1q06a_ |

### PDB 1q06 chain A

Region: 3 - 105
Aligned: 103
Modelled: 103
Confidence: 96.8%
Identity: 13%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2
5 |
| c3qaoA_ |

### PDB 3qao chain A

Region: 3 - 48
Aligned: 46
Modelled: 45
Confidence: 96.2%
Identity: 26%
PDB header:transcription regulator
Chain: A: PDB Molecule:merr-like transcriptional regulator;
PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e

Phyre2
6 |
| c2zhhA_ |

### PDB 2zhh chain A

Region: 3 - 36
Aligned: 34
Modelled: 34
Confidence: 96.2%
Identity: 9%
PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr

Phyre2
7 |
| c3gp4B_ |

### PDB 3gp4 chain B

Region: 3 - 48
Aligned: 46
Modelled: 46
Confidence: 96.1%
Identity: 15%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes

Phyre2
8 |
| c2vz4A_ |

### PDB 2vz4 chain A

Region: 3 - 48
Aligned: 46
Modelled: 46
Confidence: 96.1%
Identity: 20%
PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional activator tipa;
PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna

Phyre2
9 |
| d1r8ea1 |

### PDB 1r8e chain A domain 1

Region: 4 - 160
Aligned: 108
Modelled: 108
Confidence: 96.0%
Identity: 13%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2
10 |
| c3bd1B_ |

### PDB 3bd1 chain B

Region: 4 - 32
Aligned: 29
Modelled: 29
Confidence: 95.8%
Identity: 24%
PDB header:transcription
Chain: B: PDB Molecule:cro protein;
PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1

Phyre2
11 |
| c2jmlA_ |

### PDB 2jml chain A

Region: 1 - 48
Aligned: 48
Modelled: 48
Confidence: 95.7%
Identity: 21%
PDB header:transcription
Chain: A: PDB Molecule:dna binding domain/transcriptional regulator;
PDBTitle: solution structure of the n-terminal domain of cara repressor

Phyre2
12 |
| d2ppxa1 |

### PDB 2ppx chain A domain 1

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 95.6%
Identity: 7%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: SinR domain-like

Phyre2
13 |
| c2ppxA_ |

### PDB 2ppx chain A

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 95.6%
Identity: 7%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein atu1735;
PDBTitle: crystal structure of a hth xre-family like protein from agrobacterium2 tumefaciens

Phyre2
14 |
| c3gpvA_ |

### PDB 3gpv chain A

Region: 4 - 48
Aligned: 45
Modelled: 45
Confidence: 95.6%
Identity: 16%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis

Phyre2
15 |
| c2fjrB_ |

### PDB 2fjr chain B

Region: 4 - 29
Aligned: 26
Modelled: 26
Confidence: 95.3%
Identity: 27%
PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186

Phyre2
16 |
| c3fmyA_ |

### PDB 3fmy chain A

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 95.2%
Identity: 17%
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)

Phyre2
17 |
| c3gn5B_ |

### PDB 3gn5 chain B

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 94.4%
Identity: 17%
PDB header:dna binding protein
Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021);
PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)

Phyre2
18 |
| d1biaa1 |

### PDB 1bia chain A domain 1

Region: 3 - 36
Aligned: 34
Modelled: 34
Confidence: 93.7%
Identity: 29%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2
19 |
| c2ebyA_ |

### PDB 2eby chain A

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 93.7%
Identity: 7%
PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli

Phyre2
20 |
| c2kpjA_ |

### PDB 2kpj chain A

Region: 2 - 29
Aligned: 28
Modelled: 28
Confidence: 93.5%
Identity: 21%
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

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1j9ia_ |
|  | 99.5 | 100 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Terminase gpNU1 subunit domain
2 | c3hh0C_ |
|  | 97.1 | 12 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus
3 | d1r8da_ |
|  | 96.9 | 27 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
4 | d1q06a_ |
|  | 96.8 | 13 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
5 | c3qaoA_ |
|  | 96.2 | 26 | PDB header:transcription regulator Chain: A: PDB Molecule:merr-like transcriptional regulator; PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e
6 | c2zhhA_ |
|  | 96.2 | 9 | PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr
7 | c3gp4B_ |
|  | 96.1 | 15 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes
8 | c2vz4A_ |
|  | 96.1 | 20 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator tipa; PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna
9 | d1r8ea1 |
|  | 96.0 | 13 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
10 | c3bd1B_ |
|  | 95.8 | 24 | PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1
11 | c2jmlA_ |
|  | 95.7 | 21 | PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor
12 | d2ppxa1 |
|  | 95.6 | 7 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
13 | c2ppxA_ |
|  | 95.6 | 7 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1735; PDBTitle: crystal structure of a hth xre-family like protein from agrobacterium2 tumefaciens
14 | c3gpvA_ |
|  | 95.6 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
15 | c2fjrB_ |
|  | 95.3 | 27 | PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186
16 | c3fmyA_ |
|  | 95.2 | 17 | 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)
17 | c3gn5B_ |
|  | 94.4 | 17 | PDB header:dna binding protein Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021); PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
18 | d1biaa1 |
|  | 93.7 | 29 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
19 | c2ebyA_ |
|  | 93.7 | 7 | PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli
20 | c2kpjA_ |
|  | 93.5 | 21 | 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
21 | d2croa_ |
| not modelled | 93.4 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
22 | c2xcjB_ |
| not modelled | 93.4 | 21 | PDB header:viral protein Chain: B: PDB Molecule:c protein; PDBTitle: crystal structure of p2 c, the immunity repressor of2 temperate e. coli phage p2
23 | d1r69a_ |
| not modelled | 93.2 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
24 | d1sq8a_ |
| not modelled | 93.2 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
25 | c3omtA_ |
| not modelled | 93.1 | 11 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae.
26 | c1z4hA_ |
| not modelled | 93.0 | 9 | PDB header:protein binding, dna binding protein Chain: A: PDB Molecule:tor inhibition protein; PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase
27 | c3op9A_ |
| not modelled | 92.9 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua
28 | c3mlfC_ |
| not modelled | 92.8 | 34 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: putative transcriptional regulator from staphylococcus aureus.
29 | c2jvlA_ |
| not modelled | 92.8 | 11 | PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
30 | c1u78A_ |
| not modelled | 92.7 | 8 | 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
31 | c1zvvA_ |
| not modelled | 92.6 | 20 | PDB header:transcription/dna Chain: A: PDB Molecule:glucose-resistance amylase regulator; PDBTitle: crystal structure of a ccpa-crh-dna complex
32 | c3bs3A_ |
| not modelled | 92.5 | 24 | 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
33 | d1x57a1 |
| not modelled | 92.3 | 14 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like
34 | d1i5za1 |
| not modelled | 92.3 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
35 | c2kfsA_ |
| not modelled | 92.3 | 15 | PDB header:dna-binding protein Chain: A: PDB Molecule:conserved hypothetical regulatory protein; PDBTitle: nmr structure of rv2175c
36 | d1ft9a1 |
| not modelled | 92.1 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
37 | d1llib_ |
| not modelled | 92.0 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
38 | c3cecA_ |
| not modelled | 91.9 | 28 | PDB header:transcription Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system; PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution
39 | c3trbA_ |
| not modelled | 91.8 | 10 | 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
40 | d2h6ca1 |
| not modelled | 91.7 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
41 | c2w48D_ |
| not modelled | 91.6 | 21 | PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
42 | d1rzsa_ |
| not modelled | 91.6 | 16 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
43 | d2icta1 |
| not modelled | 91.1 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
44 | d2oz6a1 |
| not modelled | 91.1 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
45 | d1b0na2 |
| not modelled | 90.9 | 12 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
46 | c3dnvB_ |
| not modelled | 90.9 | 24 | PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein
47 | d1hlva1 |
| not modelled | 90.9 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
48 | c3ivpD_ |
| not modelled | 90.8 | 14 | PDB header:dna binding protein Chain: D: PDB Molecule:putative transposon-related dna-binding protein; PDBTitle: the structure of a possible transposon-related dna-binding protein2 from clostridium difficile 630.
49 | c2ef8A_ |
| not modelled | 90.8 | 17 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcription factor; PDBTitle: crystal structure of c.ecot38is
50 | c3f52A_ |
| not modelled | 90.8 | 18 | PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum
51 | d3e5ua1 |
| not modelled | 90.6 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
52 | c2dg6A_ |
| not modelled | 90.6 | 34 | PDB header:gene regulation Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of the putative transcriptional regulator sco55502 from streptomyces coelicolor a3(2)
53 | c3d6zA_ |
| not modelled | 90.6 | 6 | PDB header:transcription regulator/dna Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator; PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine
54 | d1j5ya1 |
| not modelled | 90.6 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
55 | d2a6ca1 |
| not modelled | 90.6 | 8 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354
56 | d2coha1 |
| not modelled | 90.6 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
57 | c1b0nA_ |
| not modelled | 90.6 | 12 | PDB header:transcription regulator Chain: A: PDB Molecule:protein (sinr protein); PDBTitle: sinr protein/sini protein complex
58 | d1lmb3_ |
| not modelled | 90.5 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
59 | d1rioa_ |
| not modelled | 90.5 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
60 | d1ic8a2 |
| not modelled | 90.2 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain
61 | d2gaua1 |
| not modelled | 90.2 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
62 | c2o38A_ |
| not modelled | 90.0 | 8 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: putative xre family transcriptional regulator
63 | d2o38a1 |
| not modelled | 90.0 | 8 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354
64 | d1k78a1 |
| not modelled | 89.9 | 8 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
65 | d1adra_ |
| not modelled | 89.9 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
66 | d2r1jl1 |
| not modelled | 89.9 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
67 | c3t76A_ |
| not modelled | 89.8 | 18 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii
68 | d1y9qa1 |
| not modelled | 89.7 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain
69 | d2bgca1 |
| not modelled | 89.7 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
70 | c1y9qA_ |
| not modelled | 89.6 | 11 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, hth_3 family; PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae
71 | c6paxA_ |
| not modelled | 89.6 | 8 | 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
72 | d2b5aa1 |
| not modelled | 89.5 | 21 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
73 | d1pdnc_ |
| not modelled | 89.3 | 4 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
74 | c3kxaD_ |
| not modelled | 89.2 | 11 | PDB header:structural genomics, unknown function Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae
75 | c3bwgA_ |
| not modelled | 89.2 | 21 | 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
76 | c2elhA_ |
| not modelled | 89.0 | 21 | 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
77 | c3clcC_ |
| not modelled | 89.0 | 11 | PDB header:transcription regulator/dna Chain: C: PDB Molecule:regulatory protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator
78 | c1hlvA_ |
| not modelled | 88.7 | 17 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:major centromere autoantigen b; PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna
79 | d6paxa1 |
| not modelled | 88.6 | 8 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
80 | d1utxa_ |
| not modelled | 88.6 | 17 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
81 | c3neuA_ |
| not modelled | 88.6 | 9 | 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
82 | d2jn6a1 |
| not modelled | 88.4 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like
83 | c3f8mA_ |
| not modelled | 88.3 | 19 | PDB header:transcription Chain: A: PDB Molecule:gntr-family protein transcriptional regulator; PDBTitle: crystal structure of phnf from mycobacterium smegmatis
84 | c3b7hA_ |
| not modelled | 88.3 | 17 | PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11
85 | c3eusB_ |
| not modelled | 88.1 | 7 | PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
86 | c2du9A_ |
| not modelled | 88.0 | 24 | PDB header:transcription Chain: A: PDB Molecule:predicted transcriptional regulators; PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
87 | c3by6C_ |
| not modelled | 88.0 | 12 | PDB header:transcription regulator Chain: C: PDB Molecule:predicted transcriptional regulator; PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
88 | c3eetA_ |
| not modelled | 88.0 | 17 | PDB header:transcription regulator Chain: A: PDB Molecule:putative gntr-family transcriptional regulator; PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
89 | c2di3A_ |
| not modelled | 87.9 | 15 | PDB header:transcription Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family; PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum
90 | d1y7ya1 |
| not modelled | 87.9 | 14 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
91 | c3fmsA_ |
| not modelled | 87.6 | 13 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: crystal structure of tm0439, a gntr transcriptional2 regulator
92 | d1bw6a_ |
| not modelled | 87.3 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
93 | d1pm6a_ |
| not modelled | 87.2 | 17 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like
94 | c2ewtA_ |
| not modelled | 86.9 | 7 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd
95 | c3edpB_ |
| not modelled | 86.8 | 32 | 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
96 | c2hs5A_ |
| not modelled | 86.3 | 9 | 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
97 | c2bgcA_ |
| not modelled | 86.1 | 15 | PDB header:transcription Chain: A: PDB Molecule:prfa; PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes
98 | c3f6wE_ |
| not modelled | 86.0 | 14 | PDB header:dna binding protein Chain: E: PDB Molecule:xre-family like protein; PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000
99 | d1hw1a1 |
| not modelled | 86.0 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
100 | d3ctaa1 |
| not modelled | 85.6 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
101 | d2p7vb1 |
| not modelled | 85.4 | 8 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
102 | c3kjxD_ |
| not modelled | 85.3 | 15 | PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator, laci family; PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi
103 | d2ofya1 |
| not modelled | 85.3 | 17 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
104 | c3c7jA_ |
| not modelled | 85.2 | 14 | 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
105 | d1lcda_ |
| not modelled | 84.8 | 28 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
106 | d1xsva_ |
| not modelled | 84.6 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
107 | d1rp3a2 |
| not modelled | 84.3 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
108 | c2o8xA_ |
| not modelled | 84.3 | 16 | PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc
109 | d1z6ra1 |
| not modelled | 84.3 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain
110 | d1stza1 |
| not modelled | 84.3 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain
111 | d2isya1 |
| not modelled | 84.1 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
112 | c1e2xA_ |
| not modelled | 84.0 | 15 | PDB header:transcriptional regulation Chain: A: PDB Molecule:fatty acid metabolism regulator protein; PDBTitle: fadr, fatty acid responsive transcription factor from e.2 coli
113 | d1g3wa1 |
| not modelled | 83.9 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
114 | d2ao9a1 |
| not modelled | 83.8 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Nanomeric phage protein-like
115 | c1j5yA_ |
| not modelled | 83.8 | 32 | 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
116 | d3bwga1 |
| not modelled | 83.6 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators
117 | d1ku7a_ |
| not modelled | 83.4 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
118 | c3mkyP_ |
| not modelled | 83.4 | 12 | PDB header:dna binding protein/dna Chain: P: PDB Molecule:protein sopb; PDBTitle: structure of sopb(155-323)-18mer dna complex, i23 form
119 | d1z05a1 |
| not modelled | 83.3 | 8 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain
120 | c2bnoA_ |
| not modelled | 83.3 | 21 | PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.

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