Phyre 2 Results for P31449

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Email | l.a.kelley@imperial.ac.uk
Description | P31449
Date | Thu Jan 5 11:47:40 GMT 2012
Unique Job ID | 9e7a0531b882568e

Summary |

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

Model (left) based on template c3gbgA_
Top template information
PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395
Confidence and coverage
Confidence: | 100.0% | Coverage: | 77%
228 residues ( 77% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | N | G | K | L | Q | S | S | D | V | K | N | E | T | P | Y | N | I | P | L | L | I | N | E | N | V | I | S | S | G | I | S | L | I | S | L | W | H | T | Y | A | D | E | H | Y | R | V | I | W | P | R | D | K | K | K | P | L | I | A | N
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | W | V | A | V | Y | T | V | Q | G | C | G | K | I | L | L | K | N | G | E | Q | I | T | L | H | G | N | C | I | I | F | L | K | P | M | D | I | H | S | Y | H | C | E | G | L | V | W | E | Q | Y | W | M | E | F | T | P | T | S | M | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | D | I | P | V | G | Q | Q | S | V | I | Y | N | G | E | I | Y | N | Q | E | L | T | E | V | A | E | L | I | T | S | P | E | A | I | K | N | N | L | A | V | A | F | L | T | K | I | I | Y | Q | W | I | C | L | M | Y | A | D | G | K | K | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | P | Q | R | R | Q | I | E | K | L | I | A | T | L | H | A | S | L | Q | Q | R | W | S | V | A | D | M | A | A | T | I | P | C | S | E | A | W | L | R | R | L | F | L | R | Y | T | G | K | T | P | K | E | Y | Y | L | D | A | R | L | D | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | .
Sequence |  | A | L | S | L | L | K | Q | Q | G | N | S | V | G | E | V | A | D | T | L | N | F | F | D | S | F | H | F | S | K | A | F | K | H | K | F | G | Y | A | P | S | A | V | L | K | N | T | D | Q | H | P | T | D | A | S | P | H | N
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 |
| c3gbgA_ |

### PDB 3gbg chain A

Region: 57 - 285
Aligned: 228
Modelled: 229
Confidence: 100.0%
Identity: 16%
PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395

Phyre2
2 |
| c1d5yD_ |

### PDB 1d5y chain D

Region: 182 - 295
Aligned: 114
Modelled: 114
Confidence: 99.9%
Identity: 25%
PDB header:transcription/dna
Chain: D: PDB Molecule:rob transcription factor;
PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna

Phyre2
3 |
| c1bl0A_ |

### PDB 1bl0 chain A

Region: 182 - 297
Aligned: 114
Modelled: 116
Confidence: 99.9%
Identity: 17%
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex

Phyre2
4 |
| c3oioA_ |

### PDB 3oio chain A

Region: 179 - 290
Aligned: 112
Modelled: 112
Confidence: 99.9%
Identity: 26%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain-
PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum

Phyre2
5 |
| c3oouA_ |

### PDB 3oou chain A

Region: 186 - 287
Aligned: 102
Modelled: 102
Confidence: 99.9%
Identity: 19%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua

Phyre2
6 |
| c2k9sA_ |

### PDB 2k9s chain A

Region: 184 - 287
Aligned: 104
Modelled: 104
Confidence: 99.9%
Identity: 22%
PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac

Phyre2
7 |
| c3mn2B_ |

### PDB 3mn2 chain B

Region: 184 - 288
Aligned: 105
Modelled: 105
Confidence: 99.9%
Identity: 21%
PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009

Phyre2
8 |
| c3mklB_ |

### PDB 3mkl chain B

Region: 178 - 288
Aligned: 110
Modelled: 111
Confidence: 99.9%
Identity: 17%
PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12

Phyre2
9 |
| c3lsgD_ |

### PDB 3lsg chain D

Region: 187 - 275
Aligned: 89
Modelled: 89
Confidence: 99.8%
Identity: 21%
PDB header:transcription regulator
Chain: D: PDB Molecule:two-component response regulator yesn;
PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586

Phyre2
10 |
| d1d5ya2 |

### PDB 1d5y chain A domain 2

Region: 237 - 295
Aligned: 59
Modelled: 59
Confidence: 99.5%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
11 |
| d1bl0a2 |

### PDB 1bl0 chain A domain 2

Region: 237 - 295
Aligned: 59
Modelled: 59
Confidence: 99.5%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
12 |
| d2arca_ |

### PDB 2arc chain A

Region: 55 - 177
Aligned: 122
Modelled: 123
Confidence: 99.2%
Identity: 16%
Fold: Double-stranded beta-helix
Superfamily: Regulatory protein AraC
Family: Regulatory protein AraC

Phyre2
13 |
| d1bl0a1 |

### PDB 1bl0 chain A domain 1

Region: 182 - 234
Aligned: 53
Modelled: 53
Confidence: 99.0%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
14 |
| d1d5ya1 |

### PDB 1d5y chain A domain 1

Region: 182 - 234
Aligned: 53
Modelled: 53
Confidence: 99.0%
Identity: 30%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
15 |
| c1zgwA_ |

### PDB 1zgw chain A

Region: 183 - 240
Aligned: 56
Modelled: 58
Confidence: 98.9%
Identity: 25%
PDB header:transcription regulator/dna
Chain: A: PDB Molecule:ada polyprotein;
PDBTitle: nmr structure of e. coli ada protein in complex with dna

Phyre2
16 |
| c3ibmB_ |

### PDB 3ibm chain B

Region: 44 - 113
Aligned: 69
Modelled: 70
Confidence: 98.3%
Identity: 16%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of cupin 2 domain-containing protein hhal_0468 from2 halorhodospira halophila

Phyre2
17 |
| c3kgzA_ |

### PDB 3kgz chain A

Region: 44 - 113
Aligned: 69
Modelled: 70
Confidence: 98.1%
Identity: 16%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein;
PDBTitle: crystal structure of a cupin 2 conserved barrel domain protein from2 rhodopseudomonas palustris

Phyre2
18 |
| c3h7yA_ |

### PDB 3h7y chain A

Region: 56 - 116
Aligned: 60
Modelled: 61
Confidence: 98.1%
Identity: 12%
PDB header:biosynthetic protein
Chain: A: PDB Molecule:bacilysin biosynthesis protein bacb;
PDBTitle: crystal structure of bacb, an enzyme involved in bacilysin synthesis,2 in tetragonal form

Phyre2
19 |
| c3jzvA_ |

### PDB 3jzv chain A

Region: 45 - 113
Aligned: 68
Modelled: 67
Confidence: 98.0%
Identity: 9%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein rru_a2000;
PDBTitle: crystal structure of rru_a2000 from rhodospirillum rubrum: a cupin-22 domain.

Phyre2
20 |
| c2d40C_ |

### PDB 2d40 chain C

Region: 44 - 122
Aligned: 79
Modelled: 79
Confidence: 98.0%
Identity: 14%
PDB header:oxidoreductase
Chain: C: PDB Molecule:putative gentisate 1,2-dioxygenase;
PDBTitle: crystal structure of z3393 from escherichia coli o157:h7

Phyre2
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25 |
| d1yfua1 |

### PDB 1yfu chain A domain 1

Region: 10 - 113
Aligned: 104
Modelled: 104
Confidence: 97.8%
Identity: 19%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: 3-hydroxyanthranilic acid dioxygenase-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3gbgA_ |
|  | 100.0 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395
2 | c1d5yD_ |
|  | 99.9 | 25 | PDB header:transcription/dna Chain: D: PDB Molecule:rob transcription factor; PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna
3 | c1bl0A_ |
|  | 99.9 | 17 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
4 | c3oioA_ |
|  | 99.9 | 26 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain- PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum
5 | c3oouA_ |
|  | 99.9 | 19 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua
6 | c2k9sA_ |
|  | 99.9 | 22 | PDB header:transcription Chain: A: PDB Molecule:arabinose operon regulatory protein; PDBTitle: solution structure of dna binding domain of e. coli arac
7 | c3mn2B_ |
|  | 99.9 | 21 | PDB header:transcription regulator Chain: B: PDB Molecule:probable arac family transcriptional regulator; PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009
8 | c3mklB_ |
|  | 99.9 | 17 | PDB header:transcription regulator Chain: B: PDB Molecule:hth-type transcriptional regulator gadx; PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
9 | c3lsgD_ |
|  | 99.8 | 21 | PDB header:transcription regulator Chain: D: PDB Molecule:two-component response regulator yesn; PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586
10 | d1d5ya2 |
|  | 99.5 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
11 | d1bl0a2 |
|  | 99.5 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
12 | d2arca_ |
|  | 99.2 | 16 | Fold:Double-stranded beta-helix Superfamily:Regulatory protein AraC Family:Regulatory protein AraC
13 | d1bl0a1 |
|  | 99.0 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
14 | d1d5ya1 |
|  | 99.0 | 30 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
15 | c1zgwA_ |
|  | 98.9 | 25 | PDB header:transcription regulator/dna Chain: A: PDB Molecule:ada polyprotein; PDBTitle: nmr structure of e. coli ada protein in complex with dna
16 | c3ibmB_ |
|  | 98.3 | 16 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of cupin 2 domain-containing protein hhal_0468 from2 halorhodospira halophila
17 | c3kgzA_ |
|  | 98.1 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein; PDBTitle: crystal structure of a cupin 2 conserved barrel domain protein from2 rhodopseudomonas palustris
18 | c3h7yA_ |
|  | 98.1 | 12 | PDB header:biosynthetic protein Chain: A: PDB Molecule:bacilysin biosynthesis protein bacb; PDBTitle: crystal structure of bacb, an enzyme involved in bacilysin synthesis,2 in tetragonal form
19 | c3jzvA_ |
|  | 98.0 | 9 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein rru_a2000; PDBTitle: crystal structure of rru_a2000 from rhodospirillum rubrum: a cupin-22 domain.
20 | c2d40C_ |
|  | 98.0 | 14 | PDB header:oxidoreductase Chain: C: PDB Molecule:putative gentisate 1,2-dioxygenase; PDBTitle: crystal structure of z3393 from escherichia coli o157:h7
21 | d1y9qa2 |
| not modelled | 97.9 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Probable transcriptional regulator VC1968, C-terminal domain
22 | d3bu7a1 |
| not modelled | 97.9 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Gentisate 1,2-dioxygenase-like
23 | c3bu7A_ |
| not modelled | 97.9 | 12 | PDB header:oxidoreductase Chain: A: PDB Molecule:gentisate 1,2-dioxygenase; PDBTitle: crystal structure and biochemical characterization of gdosp,2 a gentisate 1,2-dioxygenase from silicibacter pomeroyi
24 | d2d40a1 |
| not modelled | 97.9 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Gentisate 1,2-dioxygenase-like
25 | d1yfua1 |
|  | 97.8 | 19 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like
26 | d2f4pa1 |
| not modelled | 97.8 | 9 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
27 | d1vj2a_ |
| not modelled | 97.8 | 16 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1459-like
28 | d1y3ta1 |
| not modelled | 97.8 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Quercetin 2,3-dioxygenase-like
29 | c3cewA_ |
| not modelled | 97.8 | 13 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized cupin protein; PDBTitle: crystal structure of a cupin protein (bf4112) from bacteroides2 fragilis. northeast structural genomics consortium target bfr205
30 | c3rnsA_ |
| not modelled | 97.8 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein; PDBTitle: cupin 2 conserved barrel domain protein from leptotrichia buccalis
31 | d1sefa_ |
| not modelled | 97.8 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
32 | c1sefA_ |
| not modelled | 97.8 | 14 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: crystal structure of cupin domain protein ef2996 from enterococcus2 faecalis
33 | c3fjsC_ |
| not modelled | 97.8 | 14 | PDB header:biosynthetic protein Chain: C: PDB Molecule:uncharacterized protein with rmlc-like cupin fold; PDBTitle: crystal structure of a putative biosynthetic protein with rmlc-like2 cupin fold (reut_b4087) from ralstonia eutropha jmp134 at 1.90 a3 resolution
34 | d1sfna_ |
| not modelled | 97.8 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
35 | c2ozjB_ |
| not modelled | 97.8 | 12 | PDB header:unknown function Chain: B: PDB Molecule:cupin 2, conserved barrel; PDBTitle: crystal structure of a cupin superfamily protein (dsy2733) from2 desulfitobacterium hafniense dcb-2 at 1.60 a resolution
36 | d2phda1 |
| not modelled | 97.7 | 10 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Gentisate 1,2-dioxygenase-like
37 | c2gu9B_ |
| not modelled | 97.7 | 15 | PDB header:immune system Chain: B: PDB Molecule:tetracenomycin polyketide synthesis protein; PDBTitle: crystal structure of xc5357 from xanthomonas campestris: a2 putative tetracenomycin polyketide synthesis protein3 adopting a novel cupin subfamily structure
38 | d1o4ta_ |
| not modelled | 97.7 | 17 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
39 | d1rc6a_ |
| not modelled | 97.7 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
40 | d2b8ma1 |
| not modelled | 97.7 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:MJ0764-like
41 | c2pfwB_ |
| not modelled | 97.7 | 15 | PDB header:unknown function Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of a rmlc-like cupin (sfri_3105) from shewanella2 frigidimarina ncimb 400 at 1.90 a resolution
42 | d1sq4a_ |
| not modelled | 97.6 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
43 | c2i45C_ |
| not modelled | 97.6 | 12 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis
44 | c2vpvA_ |
| not modelled | 97.6 | 5 | PDB header:cell cycle Chain: A: PDB Molecule:protein mif2; PDBTitle: dimerization domain of mif2p
45 | c2o8qA_ |
| not modelled | 97.6 | 12 | PDB header:metal binding protein Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a protein with a cupin-like fold and unknown2 function (bxe_c0505) from burkholderia xenovorans lb400 at 1.55 a3 resolution
46 | d1yhfa1 |
| not modelled | 97.6 | 11 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
47 | c3ht2A_ |
| not modelled | 97.5 | 16 | PDB header:lyase Chain: A: PDB Molecule:remf protein; PDBTitle: zink containing polyketide cyclase remf from streptomyces2 resistomycificus
48 | d1juha_ |
| not modelled | 97.5 | 10 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Quercetin 2,3-dioxygenase-like
49 | d1lr5a_ |
| not modelled | 97.5 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
50 | c3bcwB_ |
| not modelled | 97.5 | 7 | PDB header:unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a duf861 family protein with a rmlc-like cupin2 fold (bb1179) from bordetella bronchiseptica rb50 at 1.60 a3 resolution
51 | d2bnma2 |
| not modelled | 97.5 | 8 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1459-like
52 | d1uika1 |
| not modelled | 97.5 | 9 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
53 | c3d82A_ |
| not modelled | 97.5 | 10 | PDB header:metal binding protein Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of a cupin-2 domain containing protein (sfri_3543)2 from shewanella frigidimarina ncimb 400 at 2.05 a resolution
54 | c3h8uA_ |
| not modelled | 97.4 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized conserved protein with double-stranded PDBTitle: crystal structure of uncharacterized conserved protein with double-2 stranded beta-helix domain (yp_001338853.1) from klebsiella3 pneumoniae subsp. pneumoniae mgh 78578 at 1.80 a resolution
55 | d1uija1 |
| not modelled | 97.4 | 10 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
56 | d1zvfa1 |
| not modelled | 97.4 | 16 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like
57 | d1dgwa_ |
| not modelled | 97.4 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
58 | c3lwcA_ |
| not modelled | 97.4 | 8 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of structural genomics, unknown function2 (yp_766765.1) from rhizobium leguminosarum bv. viciae 3841 at 1.40 a3 resolution
59 | d1v70a_ |
| not modelled | 97.3 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
60 | c2oa2A_ |
| not modelled | 97.3 | 12 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:bh2720 protein; PDBTitle: crystal structure of bh2720 (10175341) from bacillus halodurans at2 1.41 a resolution
61 | c1y9qA_ |
| not modelled | 97.3 | 13 | 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
62 | c2vqaC_ |
| not modelled | 97.3 | 20 | PDB header:metal-binding protein Chain: C: PDB Molecule:sll1358 protein; PDBTitle: protein-folding location can regulate mn versus cu- or zn-2 binding. crystal structure of mnca.
63 | c3l2hD_ |
| not modelled | 97.2 | 16 | PDB header:isomerase Chain: D: PDB Molecule:putative sugar phosphate isomerase; PDBTitle: crystal structure of putative sugar phosphate isomerase (afe_0303)2 from acidithiobacillus ferrooxidans atcc 23270 at 1.85 a resolution
64 | d1o5ua_ |
| not modelled | 97.2 | 9 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Hypothetical protein TM1112
65 | d1j3pa_ |
| not modelled | 97.1 | 19 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Glucose-6-phosphate isomerase, GPI
66 | d1x82a_ |
| not modelled | 97.1 | 16 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Glucose-6-phosphate isomerase, GPI
67 | c3i7dB_ |
| not modelled | 97.1 | 7 | PDB header:isomerase Chain: B: PDB Molecule:sugar phosphate isomerase; PDBTitle: crystal structure of sugar phosphate isomerase from a cupin2 superfamily spo2919 from silicibacter pomeroyi (yp_168127.1) from3 silicibacter pomeroyi dss-3 at 2.30 a resolution
68 | c2q30C_ |
| not modelled | 97.1 | 8 | PDB header:unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a rmlc-like cupin protein (dde_2303) from2 desulfovibrio desulfuricans subsp. at 1.94 a resolution
69 | d1j58a_ |
| not modelled | 97.1 | 9 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
70 | d1zrra1 |
| not modelled | 97.0 | 17 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Acireductone dioxygenase
71 | c2bnoA_ |
| not modelled | 97.0 | 12 | PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
72 | d1fxza2 |
| not modelled | 97.0 | 16 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
73 | c2opkC_ |
| not modelled | 97.0 | 11 | PDB header:isomerase Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution
74 | d1fxza1 |
| not modelled | 97.0 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
75 | d2et1a1 |
| not modelled | 96.9 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
76 | c3myxA_ |
| not modelled | 96.9 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein pspto_0244; PDBTitle: crystal structure of a pspto_0244 (protein with unknown function which2 belongs to pfam duf861 family) from pseudomonas syringae pv. tomato3 str. dc3000 at 1.30 a resolution
77 | c2eaaB_ |
| not modelled | 96.8 | 10 | PDB header:plant protein Chain: B: PDB Molecule:7s globulin-3; PDBTitle: crystal structure of adzuki bean 7s globulin-3
78 | d2phla2 |
| not modelled | 96.8 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
79 | d2phla1 |
| not modelled | 96.8 | 10 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
80 | c2cauA_ |
| not modelled | 96.7 | 15 | PDB header:plant protein Chain: A: PDB Molecule:protein (canavalin); PDBTitle: canavalin from jack bean
81 | d2pyta1 |
| not modelled | 96.7 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:EutQ-like
82 | c2fqpD_ |
| not modelled | 96.7 | 12 | PDB header:metal binding protein Chain: D: PDB Molecule:hypothetical protein bp2299; PDBTitle: crystal structure of a cupin domain (bp2299) from bordetella pertussis2 tohama i at 1.80 a resolution
83 | c3es1A_ |
| not modelled | 96.6 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of protein with a cupin-like fold and unknown2 function (yp_001165807.1) from novosphingobium aromaticivorans dsm3 12444 at 1.91 a resolution
84 | c3es4B_ |
| not modelled | 96.6 | 5 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein duf861 with a rmlc-like cupin fold; PDBTitle: crystal structure of protein of unknown function (duf861) with a rmlc-2 like cupin fold (17741406) from agrobacterium tumefaciens str. c583 (dupont) at 1.64 a resolution
85 | c1cauB_ |
| not modelled | 96.6 | 17 | PDB header:seed storage protein Chain: B: PDB Molecule:canavalin; PDBTitle: determination of three crystal structures of canavalin by molecular2 replacement
86 | d1uika2 |
| not modelled | 96.5 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
87 | d1od5a1 |
| not modelled | 96.5 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
88 | d1uija2 |
| not modelled | 96.5 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
89 | c3kglB_ |
| not modelled | 96.5 | 10 | PDB header:plant protein Chain: B: PDB Molecule:cruciferin; PDBTitle: crystal structure of procruciferin, 11s globulin from2 brassica napus
90 | c1uijA_ |
| not modelled | 96.4 | 14 | PDB header:sugar binding protein Chain: A: PDB Molecule:beta subunit of beta conglycinin; PDBTitle: crystal structure of soybean beta-conglycinin beta2 homotrimer (i122m/k124w)
91 | c1fxzC_ |
| not modelled | 96.3 | 12 | PDB header:plant protein Chain: C: PDB Molecule:glycinin g1; PDBTitle: crystal structure of soybean proglycinin a1ab1b homotrimer
92 | c3kscD_ |
| not modelled | 96.3 | 12 | PDB header:plant protein Chain: D: PDB Molecule:lega class; PDBTitle: crystal structure of pea prolegumin, an 11s seed globulin2 from pisum sativum l.
93 | c2oziA_ |
| not modelled | 96.3 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein rpa4178; PDBTitle: structural genomics, the crystal structure of a putative2 protein rpa4178 from rhodopseudomonas palustris cga009
94 | d1od5a2 |
| not modelled | 96.3 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
95 | c3qacA_ |
| not modelled | 96.0 | 15 | PDB header:plant protein Chain: A: PDB Molecule:11s globulin seed storage protein; PDBTitle: structure of amaranth 11s proglobulin seed storage protein from2 amaranthus hypochondriacus l.
96 | c3ehkC_ |
| not modelled | 95.9 | 17 | PDB header:plant protein Chain: C: PDB Molecule:prunin; PDBTitle: crystal structure of pru du amandin, an allergenic protein2 from prunus dulcis
97 | c2d5fB_ |
| not modelled | 95.8 | 15 | PDB header:plant protein Chain: B: PDB Molecule:glycinin a3b4 subunit; PDBTitle: crystal structure of recombinant soybean proglycinin a3b4 subunit, its2 comparison with mature glycinin a3b4 subunit, responsible for hexamer3 assembly
98 | c3s7eB_ |
| not modelled | 95.8 | 14 | PDB header:allergen Chain: B: PDB Molecule:allergen ara h 1, clone p41b; PDBTitle: crystal structure of ara h 1
99 | c3c3vA_ |
| not modelled | 95.7 | 12 | PDB header:allergen Chain: A: PDB Molecule:arachin arah3 isoform; PDBTitle: crystal structure of peanut major allergen ara h 3
100 | c2e9qA_ |
| not modelled | 95.7 | 15 | PDB header:plant protein Chain: A: PDB Molecule:11s globulin subunit beta; PDBTitle: recombinant pro-11s globulin of pumpkin
101 | d1vr3a1 |
| not modelled | 95.6 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Acireductone dioxygenase
102 | d2hsga1 |
| not modelled | 94.3 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
103 | c3iwfA_ |
| not modelled | 93.9 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
104 | d1efaa1 |
| not modelled | 93.6 | 16 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
105 | d2bjca1 |
| not modelled | 93.6 | 18 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
106 | d1qpza1 |
| not modelled | 93.3 | 15 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
107 | c1u78A_ |
| not modelled | 93.1 | 13 | 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
108 | c2o3fC_ |
| not modelled | 93.1 | 25 | PDB header:transcription Chain: C: PDB Molecule:putative hth-type transcriptional regulator ybbh; PDBTitle: structural genomics, the crystal structure of the n-2 terminal domain of the putative transcriptional regulator3 ybbh from bacillus subtilis subsp. subtilis str. 168.
109 | d2o3fa1 |
| not modelled | 93.0 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:RpiR-like
110 | d1sgma1 |
| not modelled | 92.9 | 7 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
111 | c3ebrA_ |
| not modelled | 92.8 | 14 | PDB header:unknown function Chain: A: PDB Molecule:uncharacterized rmlc-like cupin; PDBTitle: crystal structure of an rmlc-like cupin protein (reut_a0381) from2 ralstonia eutropha jmp134 at 2.60 a resolution
112 | d1pmia_ |
| not modelled | 92.4 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Type I phosphomannose isomerase
113 | c1bdhA_ |
| not modelled | 91.7 | 15 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (purine repressor); PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
114 | c3h1yA_ |
| not modelled | 91.5 | 16 | PDB header:isomerase Chain: A: PDB Molecule:mannose-6-phosphate isomerase; PDBTitle: crystal structure of mannose 6-phosphate isomerase from2 salmonella typhimurium bound to substrate (f6p)and metal3 atom (zn)
115 | c3h5tA_ |
| not modelled | 91.3 | 19 | 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
116 | d1jt6a1 |
| not modelled | 90.8 | 7 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
117 | c1sgmA_ |
| not modelled | 90.7 | 7 | PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator yxaf; PDBTitle: crystal structure of hypothetical protein yxaf
118 | c1zvvA_ |
| not modelled | 90.5 | 16 | PDB header:transcription/dna Chain: A: PDB Molecule:glucose-resistance amylase regulator; PDBTitle: crystal structure of a ccpa-crh-dna complex
119 | d2i10a1 |
| not modelled | 90.4 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
120 | d2fbqa1 |
| not modelled | 90.4 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain

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