Phyre 2 Results for P76241

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P76241
Date | Thu Jan 5 12:21:05 GMT 2012
Unique Job ID | 132bf09bb0e326cb

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: | 89%
242 residues ( 89% 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 | M | H | R | L | N | L | N | G | Y | E | P | D | R | H | H | E | A | A | V | A | F | C | I | H | A | G | T | D | E | L | T | S | P | V | H | Q | H | R | K | G | Q | L | I | L | A | L | H | G | A | I | T | C | T | V | E | N | A | L | W
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | M | V | P | P | Q | Y | A | V | W | I | P | G | G | V | E | H | S | N | Q | V | T | A | N | A | E | L | C | F | L | F | I | E | P | S | A | V | T | M | P | T | T | C | C | T | L | K | I | S | P | L | C | R | E | L | I | L | T | L | A | N
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | R | T | T | T | Q | R | A | E | P | M | T | R | R | L | I | Q | V | L | F | D | E | L | P | Q | Q | P | Q | Q | Q | L | H | L | P | V | S | S | H | P | K | I | R | T | M | V | E | M | M | A | K | G | P | V | E | W | G | A | L | G | Q | W
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | A | G | F | F | A | M | S | E | R | N | L | A | R | L | I | V | K | E | T | G | L | S | F | R | Q | W | R | Q | Q | L | Q | L | I | M | A | L | Q | G | L | V | K | G | D | T | V | Q | K | V | A | H | T | L | G | Y | D | S | T | T | A | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | .
Sequence |  | I | T | M | F | K | K | G | L | G | Q | T | P | G | R | Y | I | A | R | L | T | T | V | S | P | Q | S | A | K | P | D | P | R | Q
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: 19 - 262
Aligned: 242
Modelled: 244
Confidence: 100.0%
Identity: 11%
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: 156 - 258
Aligned: 103
Modelled: 103
Confidence: 99.9%
Identity: 21%
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 |
| c3oioA_ |

### PDB 3oio chain A

Region: 153 - 262
Aligned: 110
Modelled: 110
Confidence: 99.9%
Identity: 21%
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
4 |
| c1bl0A_ |

### PDB 1bl0 chain A

Region: 159 - 269
Aligned: 111
Modelled: 111
Confidence: 99.9%
Identity: 19%
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex

Phyre2
5 |
| c3oouA_ |

### PDB 3oou chain A

Region: 157 - 260
Aligned: 104
Modelled: 104
Confidence: 99.9%
Identity: 26%
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: 157 - 260
Aligned: 104
Modelled: 104
Confidence: 99.9%
Identity: 20%
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: 157 - 261
Aligned: 105
Modelled: 105
Confidence: 99.9%
Identity: 16%
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: 152 - 261
Aligned: 109
Modelled: 110
Confidence: 99.9%
Identity: 22%
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: 161 - 248
Aligned: 88
Modelled: 88
Confidence: 99.8%
Identity: 20%
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 |
| d1bl0a2 |

### PDB 1bl0 chain A domain 2

Region: 211 - 269
Aligned: 59
Modelled: 59
Confidence: 99.5%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
11 |
| d1d5ya2 |

### PDB 1d5y chain A domain 2

Region: 211 - 269
Aligned: 59
Modelled: 59
Confidence: 99.4%
Identity: 24%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
12 |
| d1d5ya1 |

### PDB 1d5y chain A domain 1

Region: 156 - 208
Aligned: 53
Modelled: 53
Confidence: 99.1%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
13 |
| d1bl0a1 |

### PDB 1bl0 chain A domain 1

Region: 158 - 208
Aligned: 51
Modelled: 51
Confidence: 99.0%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
14 |
| c1zgwA_ |

### PDB 1zgw chain A

Region: 158 - 214
Aligned: 55
Modelled: 57
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
15 |
| c3ibmB_ |

### PDB 3ibm chain B

Region: 10 - 95
Aligned: 86
Modelled: 86
Confidence: 98.9%
Identity: 12%
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
16 |
| c3jzvA_ |

### PDB 3jzv chain A

Region: 16 - 102
Aligned: 87
Modelled: 87
Confidence: 98.7%
Identity: 21%
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
17 |
| d1o4ta_ |

### PDB 1o4t chain A

Region: 10 - 91
Aligned: 82
Modelled: 82
Confidence: 98.7%
Identity: 18%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: TM1287-like

Phyre2
18 |
| c3kgzA_ |

### PDB 3kgz chain A

Region: 16 - 102
Aligned: 87
Modelled: 87
Confidence: 98.7%
Identity: 18%
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
19 |
| c2pfwB_ |

### PDB 2pfw chain B

Region: 18 - 98
Aligned: 81
Modelled: 81
Confidence: 98.7%
Identity: 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

Phyre2
20 |
| d1vj2a_ |

### PDB 1vj2 chain A

Region: 18 - 97
Aligned: 80
Modelled: 80
Confidence: 98.6%
Identity: 16%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: TM1459-like

Phyre2
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| d2bnma2 |

### PDB 2bnm chain A domain 2

Region: 3 - 91
Aligned: 89
Modelled: 89
Confidence: 97.8%
Identity: 13%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: TM1459-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3gbgA_ |
|  | 100.0 | 11 | 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 | 21 | 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 | c3oioA_ |
|  | 99.9 | 21 | 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
4 | c1bl0A_ |
|  | 99.9 | 19 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
5 | c3oouA_ |
|  | 99.9 | 26 | 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 | 20 | 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 | 16 | 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 | 22 | 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 | 20 | 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 | d1bl0a2 |
|  | 99.5 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
11 | d1d5ya2 |
|  | 99.4 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
12 | d1d5ya1 |
|  | 99.1 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
13 | d1bl0a1 |
|  | 99.0 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
14 | 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
15 | c3ibmB_ |
|  | 98.9 | 12 | 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
16 | c3jzvA_ |
|  | 98.7 | 21 | 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.
17 | d1o4ta_ |
|  | 98.7 | 18 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
18 | c3kgzA_ |
|  | 98.7 | 18 | 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
19 | c2pfwB_ |
|  | 98.7 | 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
20 | d1vj2a_ |
|  | 98.6 | 16 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1459-like
21 | c3fjsC_ |
| not modelled | 98.6 | 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
22 | c3h7yA_ |
| not modelled | 98.6 | 18 | 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
23 | c2ozjB_ |
| not modelled | 98.6 | 13 | 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
24 | d2arca_ |
| not modelled | 98.6 | 13 | Fold:Double-stranded beta-helix Superfamily:Regulatory protein AraC Family:Regulatory protein AraC
25 | c3rnsA_ |
| not modelled | 98.5 | 13 | 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
26 | d1yhfa1 |
| not modelled | 98.5 | 11 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
27 | d2f4pa1 |
| not modelled | 98.5 | 18 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
28 | d1y3ta1 |
| not modelled | 98.5 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Quercetin 2,3-dioxygenase-like
29 | c3cewA_ |
| not modelled | 98.5 | 16 | 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 | d1sfna_ |
| not modelled | 98.5 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
31 | c3bu7A_ |
| not modelled | 98.5 | 11 | 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
32 | d3bu7a1 |
| not modelled | 98.5 | 11 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Gentisate 1,2-dioxygenase-like
33 | c2d40C_ |
| not modelled | 98.4 | 12 | PDB header:oxidoreductase Chain: C: PDB Molecule:putative gentisate 1,2-dioxygenase; PDBTitle: crystal structure of z3393 from escherichia coli o157:h7
34 | d1sq4a_ |
| not modelled | 98.4 | 11 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
35 | d1sefa_ |
| not modelled | 98.4 | 11 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
36 | c1sefA_ |
| not modelled | 98.4 | 11 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: crystal structure of cupin domain protein ef2996 from enterococcus2 faecalis
37 | d2d40a1 |
| not modelled | 98.4 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Gentisate 1,2-dioxygenase-like
38 | c2gu9B_ |
| not modelled | 98.4 | 18 | 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
39 | d2phda1 |
| not modelled | 98.4 | 11 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Gentisate 1,2-dioxygenase-like
40 | d1y9qa2 |
| not modelled | 98.4 | 9 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Probable transcriptional regulator VC1968, C-terminal domain
41 | d1yfua1 |
| not modelled | 98.4 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like
42 | d1rc6a_ |
| not modelled | 98.4 | 9 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YlbA-like
43 | d1uika1 |
| not modelled | 98.4 | 19 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
44 | d1lr5a_ |
| not modelled | 98.4 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
45 | c3d82A_ |
| not modelled | 98.4 | 16 | 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
46 | d1v70a_ |
| not modelled | 98.3 | 18 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1287-like
47 | c2i45C_ |
| not modelled | 98.3 | 13 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis
48 | c2vpvA_ |
| not modelled | 98.3 | 17 | PDB header:cell cycle Chain: A: PDB Molecule:protein mif2; PDBTitle: dimerization domain of mif2p
49 | d2b8ma1 |
| not modelled | 98.3 | 17 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:MJ0764-like
50 | c3ht2A_ |
| not modelled | 98.3 | 20 | PDB header:lyase Chain: A: PDB Molecule:remf protein; PDBTitle: zink containing polyketide cyclase remf from streptomyces2 resistomycificus
51 | c3i7dB_ |
| not modelled | 98.2 | 18 | 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
52 | c3l2hD_ |
| not modelled | 98.2 | 22 | 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
53 | c2q30C_ |
| not modelled | 98.2 | 16 | 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
54 | c2oa2A_ |
| not modelled | 98.2 | 18 | 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
55 | c2o8qA_ |
| not modelled | 98.2 | 19 | 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
56 | c3es1A_ |
| not modelled | 98.1 | 17 | 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
57 | d1zvfa1 |
| not modelled | 98.1 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like
58 | c3h8uA_ |
| not modelled | 98.1 | 8 | 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
59 | d1uika2 |
| not modelled | 98.1 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
60 | c1cauB_ |
| not modelled | 98.0 | 13 | PDB header:seed storage protein Chain: B: PDB Molecule:canavalin; PDBTitle: determination of three crystal structures of canavalin by molecular2 replacement
61 | d1dgwa_ |
| not modelled | 98.0 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
62 | c2fqpD_ |
| not modelled | 98.0 | 16 | 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
63 | d1fxza2 |
| not modelled | 98.0 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
64 | c2oziA_ |
| not modelled | 98.0 | 19 | 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
65 | d1uija1 |
| not modelled | 98.0 | 16 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
66 | c2vqaC_ |
| not modelled | 97.9 | 17 | 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.
67 | d1juha_ |
| not modelled | 97.9 | 17 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Quercetin 2,3-dioxygenase-like
68 | c3lwcA_ |
| not modelled | 97.9 | 11 | 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
69 | d1uija2 |
| not modelled | 97.9 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
70 | d2et1a1 |
| not modelled | 97.9 | 18 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
71 | d1j58a_ |
| not modelled | 97.9 | 17 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
72 | c3bcwB_ |
| not modelled | 97.9 | 10 | 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
73 | d2phla2 |
| not modelled | 97.8 | 14 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
74 | d1zrra1 |
| not modelled | 97.8 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Acireductone dioxygenase
75 | d2bnma2 |
|  | 97.8 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:TM1459-like
76 | d1j3pa_ |
| not modelled | 97.8 | 20 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Glucose-6-phosphate isomerase, GPI
77 | d1fxza1 |
| not modelled | 97.8 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
78 | c1y9qA_ |
| not modelled | 97.8 | 8 | 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
79 | d1x82a_ |
| not modelled | 97.7 | 19 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Glucose-6-phosphate isomerase, GPI
80 | d1od5a2 |
| not modelled | 97.6 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
81 | c1uijA_ |
| not modelled | 97.6 | 19 | 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)
82 | d1od5a1 |
| not modelled | 97.6 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
83 | d1o5ua_ |
| not modelled | 97.5 | 12 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Hypothetical protein TM1112
84 | c1fxzC_ |
| not modelled | 97.5 | 14 | PDB header:plant protein Chain: C: PDB Molecule:glycinin g1; PDBTitle: crystal structure of soybean proglycinin a1ab1b homotrimer
85 | d2phla1 |
| not modelled | 97.4 | 17 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein
86 | c2cauA_ |
| not modelled | 97.4 | 17 | PDB header:plant protein Chain: A: PDB Molecule:protein (canavalin); PDBTitle: canavalin from jack bean
87 | c2e9qA_ |
| not modelled | 97.4 | 13 | PDB header:plant protein Chain: A: PDB Molecule:11s globulin subunit beta; PDBTitle: recombinant pro-11s globulin of pumpkin
88 | c3kglB_ |
| not modelled | 97.4 | 13 | PDB header:plant protein Chain: B: PDB Molecule:cruciferin; PDBTitle: crystal structure of procruciferin, 11s globulin from2 brassica napus
89 | c3s7eB_ |
| not modelled | 97.4 | 12 | PDB header:allergen Chain: B: PDB Molecule:allergen ara h 1, clone p41b; PDBTitle: crystal structure of ara h 1
90 | c3kscD_ |
| not modelled | 97.3 | 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.
91 | c2eaaB_ |
| not modelled | 97.2 | 16 | PDB header:plant protein Chain: B: PDB Molecule:7s globulin-3; PDBTitle: crystal structure of adzuki bean 7s globulin-3
92 | c2bnoA_ |
| not modelled | 97.2 | 12 | PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
93 | d2pyta1 |
| not modelled | 97.2 | 11 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:EutQ-like
94 | c2opkC_ |
| not modelled | 97.1 | 15 | 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
95 | c3c3vA_ |
| not modelled | 97.1 | 12 | PDB header:allergen Chain: A: PDB Molecule:arachin arah3 isoform; PDBTitle: crystal structure of peanut major allergen ara h 3
96 | c2d5fB_ |
| not modelled | 97.1 | 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
97 | c3ebrA_ |
| not modelled | 97.0 | 11 | 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
98 | c3o14B_ |
| not modelled | 96.9 | 20 | PDB header:gene regulation Chain: B: PDB Molecule:anti-ecfsigma factor, chrr; PDBTitle: crystal structure of an anti-ecfsigma factor, chrr (maqu_0586) from2 marinobacter aquaeolei vt8 at 1.70 a resolution
99 | c3ehkC_ |
| not modelled | 96.9 | 19 | PDB header:plant protein Chain: C: PDB Molecule:prunin; PDBTitle: crystal structure of pru du amandin, an allergenic protein2 from prunus dulcis
100 | d1vr3a1 |
| not modelled | 96.8 | 10 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Acireductone dioxygenase
101 | c3myxA_ |
| not modelled | 96.7 | 12 | 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
102 | c2xlfA_ |
| not modelled | 96.7 | 17 | PDB header:metal binding protein Chain: A: PDB Molecule:sll1785 protein; PDBTitle: structure and metal-loading of a soluble periplasm cupro-protein:2 apo-cuca-closed (semet)
103 | c3balB_ |
| not modelled | 96.6 | 8 | PDB header:oxidoreductase Chain: B: PDB Molecule:acetylacetone-cleaving enzyme; PDBTitle: crystal structure of an acetylacetone dioxygenase from2 acinetobacter johnsonii
104 | c3cjxE_ |
| not modelled | 96.1 | 18 | PDB header:unknown function Chain: E: PDB Molecule:protein of unknown function with a cupin-like fold; PDBTitle: crystal structure of a protein of unknown function with a cupin-like2 fold (reut_b4571) from ralstonia eutropha jmp134 at 2.60 a resolution
105 | d2o1qa1 |
| not modelled | 95.8 | 9 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Acetylacetone-cleaving enzyme-like
106 | c3es4B_ |
| not modelled | 95.7 | 12 | 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
107 | c1ey2A_ |
| not modelled | 95.6 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:homogentisate 1,2-dioxygenase; PDBTitle: human homogentisate dioxygenase with fe(ii)
108 | d1eyba_ |
| not modelled | 95.5 | 18 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Homogentisate dioxygenase
109 | c2y0oA_ |
| not modelled | 95.4 | 17 | PDB header:isomerase Chain: A: PDB Molecule:probable d-lyxose ketol-isomerase; PDBTitle: the structure of a d-lyxose isomerase from the sigmab2 regulon of bacillus subtilis
110 | c2qnkA_ |
| not modelled | 95.2 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:3-hydroxyanthranilate 3,4-dioxygenase; PDBTitle: crystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase
111 | d1vrba1 |
| not modelled | 94.8 | 19 | Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:Asparaginyl hydroxylase-like
112 | d2hsga1 |
| not modelled | 94.5 | 16 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
113 | d2o3fa1 |
| not modelled | 94.5 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:RpiR-like
114 | d2pa7a1 |
| not modelled | 94.4 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:dTDP-sugar isomerase
115 | c2o3fC_ |
| not modelled | 94.4 | 18 | 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.
116 | c3iwfA_ |
| not modelled | 94.3 | 18 | 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
117 | c3mpbA_ |
| not modelled | 94.1 | 24 | PDB header:isomerase Chain: A: PDB Molecule:sugar isomerase; PDBTitle: z5688 from e. coli o157:h7 bound to fructose
118 | d1efaa1 |
| not modelled | 94.0 | 16 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator
119 | d1sgma1 |
| not modelled | 93.5 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
120 | d1tq5a1 |
| not modelled | 93.4 | 15 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Pirin-like

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]
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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