Phyre 2 Results for P76063

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Email | l.a.kelley@imperial.ac.uk
Description | P76063
Date | Thu Jan 5 12:18:02 GMT 2012
Unique Job ID | 226dd4fc37a1d153

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3bd1B_
Top template information
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
Confidence and coverage
Confidence: | 99.9% | Coverage: | 62%
61 residues ( 62% 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 | K | K | E | N | Y | S | F | K | Q | A | C | A | V | V | G | G | Q | S | A | M | A | R | L | L | G | V | S | P | P | S | V | N | Q | W | I | K | G | V | R | Q | L | P | A | E | R | C | P | A | I | E | R | A | T | R | G | E | V | L | C
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | .
Sequence |  | E | E | L | R | P | D | I | D | W | S | Y | L | R | R | S | A | C | C | S | Q | N | M | S | V | K | Q | L | N | D | S | N | K | S | S | F | D | H | T
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 |
| c3bd1B_ |

### PDB 3bd1 chain B

Region: 5 - 67
Aligned: 61
Modelled: 63
Confidence: 99.9%
Identity: 44%
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
2 |
| d1rzsa_ |

### PDB 1rzs chain A

Region: 1 - 61
Aligned: 53
Modelled: 56
Confidence: 99.4%
Identity: 32%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
3 |
| c2fjrB_ |

### PDB 2fjr chain B

Region: 6 - 63
Aligned: 55
Modelled: 58
Confidence: 98.6%
Identity: 13%
PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186

Phyre2
4 |
| d1rioa_ |

### PDB 1rio chain A

Region: 6 - 67
Aligned: 60
Modelled: 60
Confidence: 98.4%
Identity: 22%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
5 |
| d1lmb3_ |

### PDB 1lmb chain 3

Region: 5 - 68
Aligned: 62
Modelled: 64
Confidence: 98.4%
Identity: 21%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
6 |
| d1llib_ |

### PDB 1lli chain B

Region: 6 - 67
Aligned: 60
Modelled: 62
Confidence: 98.3%
Identity: 22%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
7 |
| c3cecA_ |

### PDB 3cec chain A

Region: 2 - 63
Aligned: 60
Modelled: 62
Confidence: 98.2%
Identity: 17%
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

Phyre2
8 |
| d2icta1 |

### PDB 2ict chain A domain 1

Region: 3 - 63
Aligned: 59
Modelled: 61
Confidence: 98.2%
Identity: 12%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: SinR domain-like

Phyre2
9 |
| c3bs3A_ |

### PDB 3bs3 chain A

Region: 8 - 63
Aligned: 54
Modelled: 56
Confidence: 98.2%
Identity: 17%
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

Phyre2
10 |
| c3op9A_ |

### PDB 3op9 chain A

Region: 8 - 63
Aligned: 54
Modelled: 56
Confidence: 98.2%
Identity: 19%
PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua

Phyre2
11 |
| c3omtA_ |

### PDB 3omt chain A

Region: 8 - 66
Aligned: 57
Modelled: 59
Confidence: 98.1%
Identity: 23%
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.

Phyre2
12 |
| d1adra_ |

### PDB 1adr chain A

Region: 8 - 63
Aligned: 54
Modelled: 56
Confidence: 98.0%
Identity: 20%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
13 |
| c3bdnB_ |

### PDB 3bdn chain B

Region: 6 - 63
Aligned: 56
Modelled: 58
Confidence: 98.0%
Identity: 20%
PDB header:transcription/dna
Chain: B: PDB Molecule:lambda repressor;
PDBTitle: crystal structure of the lambda repressor

Phyre2
14 |
| c2ebyA_ |

### PDB 2eby chain A

Region: 17 - 63
Aligned: 45
Modelled: 47
Confidence: 98.0%
Identity: 22%
PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli

Phyre2
15 |
| d2r1jl1 |

### PDB 2r1j chain L domain 1

Region: 8 - 63
Aligned: 54
Modelled: 56
Confidence: 98.0%
Identity: 20%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: Phage repressors

Phyre2
16 |
| c2kpjA_ |

### PDB 2kpj chain A

Region: 8 - 63
Aligned: 54
Modelled: 56
Confidence: 98.0%
Identity: 24%
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
17 |
| d2b5aa1 |

### PDB 2b5a chain A domain 1

Region: 8 - 63
Aligned: 54
Modelled: 56
Confidence: 98.0%
Identity: 19%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: SinR domain-like

Phyre2
18 |
| c3trbA_ |

### PDB 3trb chain A

Region: 17 - 63
Aligned: 45
Modelled: 47
Confidence: 97.9%
Identity: 18%
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

Phyre2
19 |
| c3f52A_ |

### PDB 3f52 chain A

Region: 6 - 63
Aligned: 56
Modelled: 58
Confidence: 97.9%
Identity: 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

Phyre2
20 |
| c3f6wE_ |

### PDB 3f6w chain E

Region: 6 - 63
Aligned: 56
Modelled: 58
Confidence: 97.9%
Identity: 21%
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

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3bd1B_ |
|  | 99.9 | 44 | 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
2 | d1rzsa_ |
|  | 99.4 | 32 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
3 | c2fjrB_ |
|  | 98.6 | 13 | PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186
4 | d1rioa_ |
|  | 98.4 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
5 | d1lmb3_ |
|  | 98.4 | 21 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
6 | d1llib_ |
|  | 98.3 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
7 | c3cecA_ |
|  | 98.2 | 17 | 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
8 | d2icta1 |
|  | 98.2 | 12 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
9 | c3bs3A_ |
|  | 98.2 | 17 | 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
10 | c3op9A_ |
|  | 98.2 | 19 | PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua
11 | c3omtA_ |
|  | 98.1 | 23 | 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.
12 | d1adra_ |
|  | 98.0 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
13 | c3bdnB_ |
|  | 98.0 | 20 | PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor
14 | c2ebyA_ |
|  | 98.0 | 22 | PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli
15 | d2r1jl1 |
|  | 98.0 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
16 | c2kpjA_ |
|  | 98.0 | 24 | 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
17 | d2b5aa1 |
|  | 98.0 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
18 | c3trbA_ |
|  | 97.9 | 18 | 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
19 | c3f52A_ |
|  | 97.9 | 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
20 | c3f6wE_ |
|  | 97.9 | 21 | 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
21 | d1y7ya1 |
| not modelled | 97.9 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
22 | d2croa_ |
| not modelled | 97.9 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
23 | c3b7hA_ |
| not modelled | 97.9 | 15 | PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11
24 | c2ewtA_ |
| not modelled | 97.8 | 20 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd
25 | d1y9qa1 |
| not modelled | 97.8 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain
26 | d1utxa_ |
| not modelled | 97.8 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
27 | c3clcC_ |
| not modelled | 97.8 | 16 | 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
28 | c3mlfC_ |
| not modelled | 97.8 | 17 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: putative transcriptional regulator from staphylococcus aureus.
29 | c3ivpD_ |
| not modelled | 97.8 | 11 | 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.
30 | d1b0na2 |
| not modelled | 97.8 | 16 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
31 | c1b0nA_ |
| not modelled | 97.7 | 17 | PDB header:transcription regulator Chain: A: PDB Molecule:protein (sinr protein); PDBTitle: sinr protein/sini protein complex
32 | c3kxaD_ |
| not modelled | 97.7 | 24 | PDB header:structural genomics, unknown function Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae
33 | d1sq8a_ |
| not modelled | 97.7 | 25 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
34 | d1r69a_ |
| not modelled | 97.7 | 24 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
35 | d1x57a1 |
| not modelled | 97.6 | 21 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like
36 | c2xcjB_ |
| not modelled | 97.6 | 11 | 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
37 | c1y9qA_ |
| not modelled | 97.5 | 22 | 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
38 | c3t76A_ |
| not modelled | 97.5 | 11 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii
39 | c3eusB_ |
| not modelled | 97.5 | 23 | PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
40 | c2jvlA_ |
| not modelled | 97.5 | 17 | PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
41 | c3lisB_ |
| not modelled | 97.4 | 22 | PDB header:transcription Chain: B: PDB Molecule:csp231i c protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.csp231i (monoclinic form)
42 | d2a6ca1 |
| not modelled | 97.3 | 24 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354
43 | d2o38a1 |
| not modelled | 97.3 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354
44 | c2o38A_ |
| not modelled | 97.3 | 23 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: putative xre family transcriptional regulator
45 | c2ppxA_ |
| not modelled | 97.1 | 11 | 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
46 | d2ppxa1 |
| not modelled | 97.1 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
47 | c2ef8A_ |
| not modelled | 97.1 | 18 | PDB header:transcription regulator Chain: A: PDB Molecule:putative transcription factor; PDBTitle: crystal structure of c.ecot38is
48 | d2ofya1 |
| not modelled | 97.0 | 13 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
49 | c3dnvB_ |
| not modelled | 96.9 | 13 | PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein
50 | d1nera_ |
| not modelled | 96.9 | 19 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
51 | d4croa_ |
| not modelled | 96.8 | 29 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
52 | c3fmyA_ |
| not modelled | 96.8 | 15 | 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)
53 | c2pijB_ |
| not modelled | 96.8 | 33 | PDB header:transcription Chain: B: PDB Molecule:prophage pfl 6 cro; PDBTitle: structure of the cro protein from prophage pfl 6 in pseudomonas2 fluorescens pf-5
54 | c2bnoA_ |
| not modelled | 96.7 | 26 | PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
55 | d1d1la_ |
| not modelled | 96.7 | 31 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
56 | d3orca_ |
| not modelled | 96.0 | 32 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
57 | d1lcda_ |
| not modelled | 96.0 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
58 | d2bjca1 |
| not modelled | 95.8 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
59 | d1qpza1 |
| not modelled | 95.7 | 24 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
60 | c2l8nA_ |
| not modelled | 95.6 | 16 | 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
61 | d2hsga1 |
| not modelled | 95.6 | 16 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
62 | d1efaa1 |
| not modelled | 95.4 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
63 | c2lcvA_ |
| not modelled | 95.3 | 16 | 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
64 | c2hinA_ |
| not modelled | 95.1 | 26 | PDB header:transcription Chain: A: PDB Molecule:repressor protein; PDBTitle: structure of n15 cro at 1.05 a: an ortholog of lambda cro2 with a completely different but equally effective3 dimerization mechanism
65 | c3gn5B_ |
| not modelled | 95.1 | 15 | 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)
66 | c1bdhA_ |
| not modelled | 94.9 | 24 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (purine repressor); PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
67 | c2wusR_ |
| not modelled | 94.6 | 9 | PDB header:structural protein Chain: R: PDB Molecule:putative uncharacterized protein; PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz
68 | d1ic8a2 |
| not modelled | 94.4 | 11 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain
69 | c3kjxD_ |
| not modelled | 94.0 | 14 | 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
70 | c1zvvA_ |
| not modelled | 93.8 | 16 | PDB header:transcription/dna Chain: A: PDB Molecule:glucose-resistance amylase regulator; PDBTitle: crystal structure of a ccpa-crh-dna complex
71 | c3h5tA_ |
| not modelled | 93.5 | 27 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, laci family; PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
72 | d1uxca_ |
| not modelled | 93.4 | 22 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
73 | c3pxpA_ |
| not modelled | 93.3 | 18 | PDB header:transcription regulator Chain: A: PDB Molecule:helix-turn-helix domain protein; PDBTitle: crystal structure of a pas and dna binding domain containing protein2 (caur_2278) from chloroflexus aurantiacus j-10-fl at 2.30 a3 resolution
74 | c2axzC_ |
| not modelled | 92.9 | 16 | PDB header:transcription Chain: C: PDB Molecule:prgx; PDBTitle: crystal structure of prgx/ccf10 complex
75 | c3k2zA_ |
| not modelled | 92.7 | 12 | PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima
76 | c1r71B_ |
| not modelled | 92.6 | 20 | 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
77 | d1uxda_ |
| not modelled | 92.2 | 24 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
78 | d1b9ma1 |
| not modelled | 92.1 | 29 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:N-terminal domain of molybdate-dependent transcriptional regulator ModE
79 | d2jn6a1 |
| not modelled | 92.1 | 28 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like
80 | d1r71a_ |
| not modelled | 91.8 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like
81 | c1u78A_ |
| not modelled | 90.8 | 19 | 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
82 | c3fymA_ |
| not modelled | 90.7 | 9 | PDB header:dna binding protein Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the 1a structure of ymfm, a putative dna-binding membrane2 protein from staphylococcus aureus
83 | c2ijlB_ |
| not modelled | 90.7 | 25 | PDB header:transcription Chain: B: PDB Molecule:molybdenum-binding transcriptional repressor; PDBTitle: the structure of a putative mode from agrobacterium tumefaciens.
84 | d1fipa_ |
| not modelled | 90.5 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
85 | c3fzvC_ |
| not modelled | 90.4 | 16 | PDB header:transcription regulator Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: crystal structure of pa01 protein, putative lysr family2 transcriptional regulator from pseudomonas aeruginosa
86 | c3t1bB_ |
| not modelled | 89.8 | 11 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: crystal structure of the full-length aphb n100e variant
87 | c3fzjC_ |
| not modelled | 89.8 | 33 | PDB header:transcription regulator Chain: C: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: tsar low resolution crystal structure, tetragonal form
88 | d2esna1 |
| not modelled | 89.6 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LysR-like transcriptional regulators
89 | c1iz1B_ |
| not modelled | 88.6 | 27 | PDB header:dna binding protein Chain: B: PDB Molecule:lysr-type regulatory protein; PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator
90 | d1vz0a1 |
| not modelled | 88.5 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like
91 | c1b9nA_ |
| not modelled | 88.5 | 29 | PDB header:transcription Chain: A: PDB Molecule:protein (mode); PDBTitle: regulator from escherichia coli
92 | d1g2ha_ |
| not modelled | 88.0 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
93 | c2elhA_ |
| not modelled | 88.0 | 25 | 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
94 | c3mkyP_ |
| not modelled | 87.9 | 21 | PDB header:dna binding protein/dna Chain: P: PDB Molecule:protein sopb; PDBTitle: structure of sopb(155-323)-18mer dna complex, i23 form
95 | c3e7lD_ |
| not modelled | 87.1 | 14 | PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
96 | d1etxa_ |
| not modelled | 87.0 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
97 | c3m1eA_ |
| not modelled | 87.0 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of benm_dbd
98 | d1bw6a_ |
| not modelled | 86.8 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
99 | c2esnC_ |
| not modelled | 86.8 | 14 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: the crystal structure of probable transcriptional regulator pa04772 from pseudomonas aeruginosa
100 | d1hlva1 |
| not modelled | 86.5 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
101 | c3mkzU_ |
| not modelled | 86.4 | 21 | PDB header:dna-binding protein/dna Chain: U: PDB Molecule:protein sopb; PDBTitle: structure of sopb(155-272)-18mer complex, p21 form
102 | c2rn7A_ |
| not modelled | 84.5 | 21 | PDB header:unknown function Chain: A: PDB Molecule:is629 orfa; PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125
103 | d1k78a1 |
| not modelled | 83.4 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
104 | d1etob_ |
| not modelled | 83.3 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
105 | d1zs4a1 |
| not modelled | 83.1 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Bacteriophage CII protein
106 | c3hhgF_ |
| not modelled | 82.5 | 19 | PDB header:transcription regulator Chain: F: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: structure of crga, a lysr-type transcriptional regulator from2 neisseria meningitidis.
107 | c1umqA_ |
| not modelled | 82.2 | 11 | PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
108 | d1umqa_ |
| not modelled | 82.2 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
109 | d1ntca_ |
| not modelled | 82.2 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
110 | d1ixca1 |
| not modelled | 81.6 | 33 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LysR-like transcriptional regulators
111 | c3ispA_ |
| not modelled | 80.7 | 30 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator PDBTitle: crystal structure of argp from mycobacterium tuberculosis
112 | d1j9ia_ |
| not modelled | 80.2 | 15 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Terminase gpNU1 subunit domain
113 | c3nzlA_ |
| not modelled | 79.5 | 19 | PDB header:transcription Chain: A: PDB Molecule:dna-binding protein satb1; PDBTitle: crystal structure of the n-terminal domain of dna-binding protein2 satb1 from homo sapiens, northeast structural genomics consortium3 target hr4435b
114 | c2h8rA_ |
| not modelled | 79.2 | 11 | PDB header:transcription activator/dna Chain: A: PDB Molecule:hepatocyte nuclear factor 1-beta; PDBTitle: hepatocyte nuclear factor 1b bound to dna: mody5 gene2 product
115 | d1g3wa1 |
| not modelled | 78.0 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein
116 | d6paxa1 |
| not modelled | 77.9 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
117 | c1hlvA_ |
| not modelled | 76.6 | 12 | 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
118 | d1pdnc_ |
| not modelled | 75.9 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain
119 | c2qfcB_ |
| not modelled | 75.7 | 11 | PDB header:transcription regulation Chain: B: PDB Molecule:plcr protein; PDBTitle: crystal structure of bacillus thuringiensis plcr complexed with papr
120 | c6paxA_ |
| not modelled | 75.4 | 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

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