Phyre 2 Results for P77245

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Email | l.a.kelley@imperial.ac.uk
Description | P77245
Date | Thu Jan 5 12:26:46 GMT 2012
Unique Job ID | 49e70d8001fb5d57

Summary |

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

Model (left) based on template c3shoA_
Top template information
PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, rpir family; PDBTitle: crystal structure of rpir transcription factor from sphaerobacter2 thermophilus (sugar isomerase domain)
Confidence and coverage
Confidence: | 99.9% | Coverage: | 64%
182 residues ( 64% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
276 residues ( 97%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | L | Y | L | T | K | I | S | N | A | G | S | E | F | T | E | N | E | Q | K | I | A | D | F | L | Q | A | N | V | S | E | L | Q | S | V | S | S | R | Q | M | A | K | Q | L | G | I | S | Q | S | S | I | V | K | F | A | Q | K | L | G | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | G | F | T | E | L | R | M | A | L | I | G | E | Y | S | A | S | R | E | K | T | N | A | T | A | L | H | L | H | S | S | I | T | S | D | D | S | L | E | V | I | A | R | K | L | N | R | E | K | E | L | A | L | E | Q | T | C | A | L | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | D | Y | A | R | L | Q | K | I | I | E | V | I | S | K | A | P | F | I | Q | I | T | G | L | G | G | S | A | L | V | G | R | D | L | S | F | K | L | M | K | I | G | Y | R | V | A | C | E | A | D | T | H | V | Q | A | T | V | S | Q | A | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | K | K | G | D | V | Q | I | A | I | S | Y | S | G | S | K | K | E | I | V | L | C | A | E | A | A | R | K | Q | G | A | T | V | I | A | I | T | S | L | T | D | S | P | L | R | R | L | A | H | F | T | L | D | T | V | S | G | E | T | E | W
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | .
Sequence |  | R | S | S | S | M | S | T | R | T | A | Q | N | S | V | T | D | L | L | F | V | G | L | V | Q | L | N | D | V | E | S | L | K | M | I | Q | R | S | S | E | L | T | Q | R | L | K
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 |
| c3shoA_ |

### PDB 3sho chain A

Region: 97 - 283
Aligned: 182
Modelled: 187
Confidence: 99.9%
Identity: 19%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, rpir family;
PDBTitle: crystal structure of rpir transcription factor from sphaerobacter2 thermophilus (sugar isomerase domain)

Phyre2
2 |
| c3fxaA_ |

### PDB 3fxa chain A

Region: 94 - 277
Aligned: 184
Modelled: 184
Confidence: 99.9%
Identity: 17%
PDB header:sugar binding protein
Chain: A: PDB Molecule:sis domain protein;
PDBTitle: crystal structure of a putative sugar-phosphate isomerase2 (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 a3 resolution

Phyre2
3 |
| c2xhzC_ |

### PDB 2xhz chain C

Region: 97 - 267
Aligned: 171
Modelled: 171
Confidence: 99.9%
Identity: 19%
PDB header:isomerase
Chain: C: PDB Molecule:arabinose 5-phosphate isomerase;
PDBTitle: probing the active site of the sugar isomerase domain from e. coli2 arabinose-5-phosphate isomerase via x-ray crystallography

Phyre2
4 |
| c3etnD_ |

### PDB 3etn chain D

Region: 96 - 277
Aligned: 182
Modelled: 182
Confidence: 99.9%
Identity: 19%
PDB header:isomerase
Chain: D: PDB Molecule:putative phosphosugar isomerase involved in capsule
PDBTitle: crystal structure of putative phosphosugar isomerase involved in2 capsule formation (yp_209877.1) from bacteroides fragilis nctc 93433 at 1.70 a resolution

Phyre2
5 |
| d1vima_ |

### PDB 1vim chain A

Region: 96 - 277
Aligned: 177
Modelled: 182
Confidence: 99.9%
Identity: 19%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2
6 |
| d1m3sa_ |

### PDB 1m3s chain A

Region: 103 - 280
Aligned: 173
Modelled: 178
Confidence: 99.9%
Identity: 18%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2
7 |
| d1jeoa_ |

### PDB 1jeo chain A

Region: 104 - 277
Aligned: 166
Modelled: 174
Confidence: 99.9%
Identity: 22%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2
8 |
| c2puwA_ |

### PDB 2puw chain A

Region: 98 - 284
Aligned: 186
Modelled: 187
Confidence: 99.8%
Identity: 13%
PDB header:transferase
Chain: A: PDB Molecule:isomerase domain of glutamine-fructose-6-phosphate
PDBTitle: the crystal structure of isomerase domain of glucosamine-6-phosphate2 synthase from candida albicans

Phyre2
9 |
| c3trjC_ |

### PDB 3trj chain C

Region: 96 - 265
Aligned: 163
Modelled: 170
Confidence: 99.8%
Identity: 18%
PDB header:isomerase
Chain: C: PDB Molecule:phosphoheptose isomerase;
PDBTitle: structure of a phosphoheptose isomerase from francisella tularensis

Phyre2
10 |
| c2zj3A_ |

### PDB 2zj3 chain A

Region: 98 - 283
Aligned: 185
Modelled: 185
Confidence: 99.8%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:glucosamine--fructose-6-phosphate
PDBTitle: isomerase domain of human glucose:fructose-6-phosphate2 amidotransferase

Phyre2
11 |
| d1x92a_ |

### PDB 1x92 chain A

Region: 97 - 265
Aligned: 163
Modelled: 169
Confidence: 99.8%
Identity: 20%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2
12 |
| d1j5xa_ |

### PDB 1j5x chain A

Region: 108 - 283
Aligned: 174
Modelled: 176
Confidence: 99.8%
Identity: 13%
Fold: SIS domain
Superfamily: SIS domain
Family: double-SIS domain

Phyre2
13 |
| d1tk9a_ |

### PDB 1tk9 chain A

Region: 96 - 262
Aligned: 161
Modelled: 166
Confidence: 99.8%
Identity: 19%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2
14 |
| c2yvaB_ |

### PDB 2yva chain B

Region: 98 - 265
Aligned: 160
Modelled: 168
Confidence: 99.8%
Identity: 19%
PDB header:dna binding protein
Chain: B: PDB Molecule:dnaa initiator-associating protein diaa;
PDBTitle: crystal structure of escherichia coli diaa

Phyre2
15 |
| d1nria_ |

### PDB 1nri chain A

Region: 77 - 268
Aligned: 187
Modelled: 192
Confidence: 99.8%
Identity: 21%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2
16 |
| c1nriA_ |

### PDB 1nri chain A

Region: 77 - 268
Aligned: 187
Modelled: 192
Confidence: 99.8%
Identity: 21%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein hi0754;
PDBTitle: crystal structure of putative phosphosugar isomerase hi0754 from2 haemophilus influenzae

Phyre2
17 |
| c2a3nA_ |

### PDB 2a3n chain A

Region: 107 - 283
Aligned: 171
Modelled: 177
Confidence: 99.8%
Identity: 19%
PDB header:sugar binding protein
Chain: A: PDB Molecule:putative glucosamine-fructose-6-phosphate aminotransferase;
PDBTitle: crystal structure of a putative glucosamine-fructose-6-phosphate2 aminotransferase (stm4540.s) from salmonella typhimurium lt2 at 1.353 a resolution

Phyre2
18 |
| d1x94a_ |

### PDB 1x94 chain A

Region: 95 - 265
Aligned: 166
Modelled: 171
Confidence: 99.8%
Identity: 16%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2
19 |
| c3fj1A_ |

### PDB 3fj1 chain A

Region: 106 - 283
Aligned: 175
Modelled: 178
Confidence: 99.7%
Identity: 18%
PDB header:isomerase
Chain: A: PDB Molecule:putative phosphosugar isomerase;
PDBTitle: crystal structure of putative phosphosugar isomerase (yp_167080.1)2 from silicibacter pomeroyi dss-3 at 1.75 a resolution

Phyre2
20 |
| c2x3yA_ |

### PDB 2x3y chain A

Region: 93 - 265
Aligned: 167
Modelled: 173
Confidence: 99.7%
Identity: 17%
PDB header:isomerase
Chain: A: PDB Molecule:phosphoheptose isomerase;
PDBTitle: crystal structure of gmha from burkholderia pseudomallei

Phyre2
21 |
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| c3iwfA_ |

### PDB 3iwf chain A

Region: 2 - 88
Aligned: 87
Modelled: 86
Confidence: 99.7%
Identity: 30%
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

Phyre2
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486 |
487 |
488 |
489 |
490 |
491 |
492 |
493 |
494 |
495 |
496 |
497 |
498 |
499 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3shoA_ |
|  | 99.9 | 19 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, rpir family; PDBTitle: crystal structure of rpir transcription factor from sphaerobacter2 thermophilus (sugar isomerase domain)
2 | c3fxaA_ |
|  | 99.9 | 17 | PDB header:sugar binding protein Chain: A: PDB Molecule:sis domain protein; PDBTitle: crystal structure of a putative sugar-phosphate isomerase2 (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 a3 resolution
3 | c2xhzC_ |
|  | 99.9 | 19 | PDB header:isomerase Chain: C: PDB Molecule:arabinose 5-phosphate isomerase; PDBTitle: probing the active site of the sugar isomerase domain from e. coli2 arabinose-5-phosphate isomerase via x-ray crystallography
4 | c3etnD_ |
|  | 99.9 | 19 | PDB header:isomerase Chain: D: PDB Molecule:putative phosphosugar isomerase involved in capsule PDBTitle: crystal structure of putative phosphosugar isomerase involved in2 capsule formation (yp_209877.1) from bacteroides fragilis nctc 93433 at 1.70 a resolution
5 | d1vima_ |
|  | 99.9 | 19 | Fold:SIS domain Superfamily:SIS domain Family:mono-SIS domain
6 | d1m3sa_ |
|  | 99.9 | 18 | Fold:SIS domain Superfamily:SIS domain Family:mono-SIS domain
7 | d1jeoa_ |
|  | 99.9 | 22 | Fold:SIS domain Superfamily:SIS domain Family:mono-SIS domain
8 | c2puwA_ |
|  | 99.8 | 13 | PDB header:transferase Chain: A: PDB Molecule:isomerase domain of glutamine-fructose-6-phosphate PDBTitle: the crystal structure of isomerase domain of glucosamine-6-phosphate2 synthase from candida albicans
9 | c3trjC_ |
|  | 99.8 | 18 | PDB header:isomerase Chain: C: PDB Molecule:phosphoheptose isomerase; PDBTitle: structure of a phosphoheptose isomerase from francisella tularensis
10 | c2zj3A_ |
|  | 99.8 | 14 | PDB header:transferase Chain: A: PDB Molecule:glucosamine--fructose-6-phosphate PDBTitle: isomerase domain of human glucose:fructose-6-phosphate2 amidotransferase
11 | d1x92a_ |
|  | 99.8 | 20 | Fold:SIS domain Superfamily:SIS domain Family:mono-SIS domain
12 | d1j5xa_ |
|  | 99.8 | 13 | Fold:SIS domain Superfamily:SIS domain Family:double-SIS domain
13 | d1tk9a_ |
|  | 99.8 | 19 | Fold:SIS domain Superfamily:SIS domain Family:mono-SIS domain
14 | c2yvaB_ |
|  | 99.8 | 19 | PDB header:dna binding protein Chain: B: PDB Molecule:dnaa initiator-associating protein diaa; PDBTitle: crystal structure of escherichia coli diaa
15 | d1nria_ |
|  | 99.8 | 21 | Fold:SIS domain Superfamily:SIS domain Family:mono-SIS domain
16 | c1nriA_ |
|  | 99.8 | 21 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein hi0754; PDBTitle: crystal structure of putative phosphosugar isomerase hi0754 from2 haemophilus influenzae
17 | c2a3nA_ |
|  | 99.8 | 19 | PDB header:sugar binding protein Chain: A: PDB Molecule:putative glucosamine-fructose-6-phosphate aminotransferase; PDBTitle: crystal structure of a putative glucosamine-fructose-6-phosphate2 aminotransferase (stm4540.s) from salmonella typhimurium lt2 at 1.353 a resolution
18 | d1x94a_ |
|  | 99.8 | 16 | Fold:SIS domain Superfamily:SIS domain Family:mono-SIS domain
19 | c3fj1A_ |
|  | 99.7 | 18 | PDB header:isomerase Chain: A: PDB Molecule:putative phosphosugar isomerase; PDBTitle: crystal structure of putative phosphosugar isomerase (yp_167080.1)2 from silicibacter pomeroyi dss-3 at 1.75 a resolution
20 | c2x3yA_ |
|  | 99.7 | 17 | PDB header:isomerase Chain: A: PDB Molecule:phosphoheptose isomerase; PDBTitle: crystal structure of gmha from burkholderia pseudomallei
21 | c3euaD_ |
| not modelled | 99.7 | 17 | PDB header:isomerase Chain: D: PDB Molecule:putative fructose-aminoacid-6-phosphate deglycase; PDBTitle: crystal structure of a putative phosphosugar isomerase (bsu32610) from2 bacillus subtilis at 1.90 a resolution
22 | c3hbaA_ |
| not modelled | 99.7 | 17 | PDB header:isomerase Chain: A: PDB Molecule:putative phosphosugar isomerase; PDBTitle: crystal structure of a putative phosphosugar isomerase (sden_2705)2 from shewanella denitrificans os217 at 2.00 a resolution
23 | c3cvjB_ |
| not modelled | 99.7 | 19 | PDB header:isomerase Chain: B: PDB Molecule:putative phosphoheptose isomerase; PDBTitle: crystal structure of a putative phosphoheptose isomerase (bh3325) from2 bacillus halodurans c-125 at 2.00 a resolution
24 | c3iwfA_ |
|  | 99.7 | 30 | 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
25 | c3g68A_ |
| not modelled | 99.7 | 12 | PDB header:isomerase Chain: A: PDB Molecule:putative phosphosugar isomerase; PDBTitle: crystal structure of a putative phosphosugar isomerase (cd3275) from2 clostridium difficile 630 at 1.80 a resolution
26 | c3tbfA_ |
| not modelled | 99.7 | 18 | PDB header:transferase Chain: A: PDB Molecule:glucosamine--fructose-6-phosphate aminotransferase PDBTitle: c-terminal domain of glucosamine-fructose-6-phosphate aminotransferase2 from francisella tularensis.
27 | d1moqa_ |
| not modelled | 99.7 | 19 | Fold:SIS domain Superfamily:SIS domain Family:double-SIS domain
28 | c2amlB_ |
| not modelled | 99.7 | 17 | PDB header:transferase Chain: B: PDB Molecule:sis domain protein; PDBTitle: crystal structure of lmo0035 protein (46906266) from listeria2 monocytogenes 4b f2365 at 1.50 a resolution
29 | c3knzA_ |
| not modelled | 99.7 | 18 | PDB header:sugar binding protein Chain: A: PDB Molecule:putative sugar binding protein; PDBTitle: crystal structure of putative sugar binding protein (np_459565.1) from2 salmonella typhimurium lt2 at 2.50 a resolution
30 | c3fkjA_ |
| not modelled | 99.7 | 19 | PDB header:isomerase Chain: A: PDB Molecule:putative phosphosugar isomerases; PDBTitle: crystal structure of a putative phosphosugar isomerase (stm_0572) from2 salmonella typhimurium lt2 at 2.12 a resolution
31 | c2decA_ |
| not modelled | 99.6 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:325aa long hypothetical protein; PDBTitle: crystal structure of the ph0510 protein from pyrococcus horikoshii ot3
32 | c1jxaA_ |
| not modelled | 99.5 | 22 | PDB header:transferase Chain: A: PDB Molecule:glucosamine 6-phosphate synthase; PDBTitle: glucosamine 6-phosphate synthase with glucose 6-phosphate
33 | c3odpA_ |
| not modelled | 99.5 | 22 | PDB header:isomerase Chain: A: PDB Molecule:putative tagatose-6-phosphate ketose/aldose isomerase; PDBTitle: crystal structure of a putative tagatose-6-phosphate ketose/aldose2 isomerase (nt01cx_0292) from clostridium novyi nt at 2.35 a3 resolution
34 | d1x9ia_ |
| not modelled | 99.5 | 23 | Fold:SIS domain Superfamily:SIS domain Family:double-SIS domain
35 | c2o3fC_ |
| not modelled | 99.4 | 20 | 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.
36 | d2o3fa1 |
| not modelled | 99.4 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:RpiR-like
37 | c3i0zB_ |
| not modelled | 99.4 | 16 | PDB header:isomerase Chain: B: PDB Molecule:putative tagatose-6-phosphate ketose/aldose isomerase; PDBTitle: crystal structure of putative putative tagatose-6-phosphate2 ketose/aldose isomerase (np_344614.1) from streptococcus pneumoniae3 tigr4 at 1.70 a resolution
38 | c3c3jA_ |
| not modelled | 99.3 | 16 | PDB header:isomerase Chain: A: PDB Molecule:putative tagatose-6-phosphate ketose/aldose isomerase; PDBTitle: crystal structure of tagatose-6-phosphate ketose/aldose isomerase from2 escherichia coli
39 | c2q8nB_ |
| not modelled | 98.2 | 21 | PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of glucose-6-phosphate isomerase (ec2 5.3.1.9) (tm1385) from thermotoga maritima at 1.82 a3 resolution
40 | c1zzgB_ |
| not modelled | 98.2 | 21 | PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of hypothetical protein tt0462 from thermus2 thermophilus hb8
41 | c3ff1B_ |
| not modelled | 97.9 | 19 | PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: structure of glucose 6-phosphate isomerase from staphylococcus aureus
42 | d1c7qa_ |
| not modelled | 97.8 | 22 | Fold:SIS domain Superfamily:SIS domain Family:Phosphoglucose isomerase, PGI
43 | d1gzda_ |
| not modelled | 97.2 | 23 | Fold:SIS domain Superfamily:SIS domain Family:Phosphoglucose isomerase, PGI
44 | c3hjbA_ |
| not modelled | 97.1 | 17 | PDB header:isomerase Chain: A: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: 1.5 angstrom crystal structure of glucose-6-phosphate isomerase from2 vibrio cholerae.
45 | c3jx9B_ |
| not modelled | 97.1 | 10 | PDB header:isomerase Chain: B: PDB Molecule:putative phosphoheptose isomerase; PDBTitle: crystal structure of putative phosphoheptose isomerase2 (yp_001815198.1) from exiguobacterium sp. 255-15 at 1.95 a resolution
46 | d1iata_ |
| not modelled | 97.1 | 19 | Fold:SIS domain Superfamily:SIS domain Family:Phosphoglucose isomerase, PGI
47 | d1lnwa_ |
| not modelled | 97.0 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
48 | c3nqoB_ |
| not modelled | 97.0 | 11 | PDB header:transcription Chain: B: PDB Molecule:marr-family transcriptional regulator; PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
49 | c3ljkA_ |
| not modelled | 97.0 | 26 | PDB header:isomerase Chain: A: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: glucose-6-phosphate isomerase from francisella tularensis.
50 | c2wu8A_ |
| not modelled | 97.0 | 21 | PDB header:isomerase Chain: A: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: structural studies of phosphoglucose isomerase from2 mycobacterium tuberculosis h37rv
51 | d1hm5a_ |
| not modelled | 96.9 | 20 | Fold:SIS domain Superfamily:SIS domain Family:Phosphoglucose isomerase, PGI
52 | c3ujhB_ |
| not modelled | 96.9 | 23 | PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of substrate-bound glucose-6-phosphate isomerase2 from toxoplasma gondii
53 | d1u0fa_ |
| not modelled | 96.9 | 24 | Fold:SIS domain Superfamily:SIS domain Family:Phosphoglucose isomerase, PGI
54 | d1q50a_ |
| not modelled | 96.8 | 24 | Fold:SIS domain Superfamily:SIS domain Family:Phosphoglucose isomerase, PGI
55 | c3bj6B_ |
| not modelled | 96.6 | 15 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of marr family transcription regulator sp03579
56 | c3nbuC_ |
| not modelled | 96.5 | 22 | PDB header:isomerase Chain: C: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of pgi glucosephosphate isomerase
57 | d3broa1 |
| not modelled | 96.5 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
58 | c2o2cB_ |
| not modelled | 96.5 | 21 | PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase, glycosomal; PDBTitle: crystal structure of phosphoglucose isomerase from t. brucei2 containing glucose-6-phosphate in the active site
59 | c1t10A_ |
| not modelled | 96.4 | 24 | PDB header:isomerase Chain: A: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: phosphoglucose isomerase from leishmania mexicana in complex with2 substrate d-fructose-6-phosphate
60 | c3pr3B_ |
| not modelled | 96.4 | 28 | PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of plasmodium falciparum glucose-6-phosphate2 isomerase (pf14_0341) in complex with fructose-6-phosphate
61 | c3kp3B_ |
| not modelled | 96.3 | 10 | PDB header:transcription regulator/antibiotic Chain: B: PDB Molecule:transcriptional regulator tcar; PDBTitle: staphylococcus epidermidis in complex with ampicillin
62 | c2nnnB_ |
| not modelled | 96.2 | 11 | PDB header:transcription Chain: B: PDB Molecule:probable transcriptional regulator; PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa
63 | c3g3zA_ |
| not modelled | 96.1 | 13 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, marr family; PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
64 | d2a61a1 |
| not modelled | 96.1 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
65 | d2etha1 |
| not modelled | 96.1 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
66 | c2fa5B_ |
| not modelled | 96.1 | 10 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator marr/emrr family; PDBTitle: the crystal structure of an unliganded multiple antibiotic-2 resistance repressor (marr) from xanthomonas campestris
67 | c2rdpA_ |
| not modelled | 96.1 | 11 | PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator marr; PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
68 | d2fbha1 |
| not modelled | 96.0 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
69 | c2gxgA_ |
| not modelled | 96.0 | 15 | PDB header:transcription Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator; PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
70 | d1yioa1 |
| not modelled | 96.0 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
71 | c2zkqb_ |
| not modelled | 96.0 | 9 | PDB header:ribosomal protein/rna Chain: B: PDB Molecule:rna expansion segment es3; PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
72 | c3frwF_ |
| not modelled | 95.9 | 14 | PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
73 | d1a04a1 |
| not modelled | 95.9 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
74 | c3k0lA_ |
| not modelled | 95.8 | 19 | PDB header:transcription regulator Chain: A: PDB Molecule:repressor protein; PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp
75 | d1s3ja_ |
| not modelled | 95.8 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
76 | c3r0aB_ |
| not modelled | 95.8 | 10 | PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
77 | c3bpxB_ |
| not modelled | 95.7 | 10 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of marr
78 | d3deua1 |
| not modelled | 95.7 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
79 | c3oopA_ |
| not modelled | 95.7 | 15 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2960 protein; PDBTitle: the structure of a protein with unknown function from listeria innocua2 clip11262
80 | c3tgnA_ |
| not modelled | 95.7 | 19 | PDB header:transcription Chain: A: PDB Molecule:adc operon repressor adcr; PDBTitle: crystal structure of the zinc-dependent marr family transcriptional2 regulator adcr in the zn(ii)-bound state
81 | c1x3uA_ |
| not modelled | 95.6 | 18 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
82 | c3gbgA_ |
| not modelled | 95.6 | 21 | PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395
83 | d1lj9a_ |
| not modelled | 95.5 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
84 | c3deuB_ |
| not modelled | 95.5 | 21 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator slya; PDBTitle: crystal structure of transcription regulatory protein slya2 from salmonella typhimurium in complex with salicylate3 ligands
85 | c3cjnA_ |
| not modelled | 95.5 | 13 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
86 | c3korD_ |
| not modelled | 95.4 | 21 | PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
87 | c3iz6A_ |
| not modelled | 95.3 | 10 | PDB header:ribosome Chain: A: PDB Molecule:40s ribosomal protein sa (s2p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
88 | d1fsea_ |
| not modelled | 95.3 | 27 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
89 | c3bjaA_ |
| not modelled | 95.3 | 12 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, marr family, putative; PDBTitle: crystal structure of putative marr-like transcription regulator2 (np_978771.1) from bacillus cereus atcc 10987 at 2.38 a resolution
90 | c2rnjA_ |
| not modelled | 95.2 | 19 | PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain
91 | c3bchA_ |
| not modelled | 95.1 | 9 | PDB header:cell adhesion, ribosomal protein Chain: A: PDB Molecule:40s ribosomal protein sa; PDBTitle: crystal structure of the human laminin receptor precursor
92 | c1s1hB_ |
| not modelled | 95.1 | 12 | PDB header:ribosome Chain: B: PDB Molecule:40s ribosomal protein s0-a; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i.
93 | c3oouA_ |
| not modelled | 95.0 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua
94 | c3kjxD_ |
| not modelled | 95.0 | 23 | 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
95 | c3mklB_ |
| not modelled | 95.0 | 9 | 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
96 | d1jhfa1 |
| not modelled | 95.0 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain
97 | c3boqB_ |
| not modelled | 95.0 | 8 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of marr family transcriptional regulator from2 silicibacter pomeroyi
98 | c2k9sA_ |
| not modelled | 94.9 | 6 | PDB header:transcription Chain: A: PDB Molecule:arabinose operon regulatory protein; PDBTitle: solution structure of dna binding domain of e. coli arac
99 | c3nrvC_ |
| not modelled | 94.9 | 13 | PDB header:transcription regulator Chain: C: PDB Molecule:putative transcriptional regulator (marr/emrr family); PDBTitle: crystal structure of marr/emrr family transcriptional regulator from2 acinetobacter sp. adp1
100 | c2krfB_ |
| not modelled | 94.9 | 21 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
101 | c2l4aA_ |
| not modelled | 94.8 | 19 | PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp
102 | c3e6mD_ |
| not modelled | 94.8 | 17 | PDB header:transcription regulator Chain: D: PDB Molecule:marr family transcriptional regulator; PDBTitle: the crystal structure of a marr family transcriptional2 regulator from silicibacter pomeroyi dss.
103 | d2fbia1 |
| not modelled | 94.8 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
104 | d1p4wa_ |
| not modelled | 94.8 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
105 | d1l3la1 |
| not modelled | 94.8 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
106 | d1jhga_ |
| not modelled | 94.8 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
107 | c1zljE_ |
| not modelled | 94.8 | 19 | PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
108 | c3mn2B_ |
| not modelled | 94.8 | 13 | 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
109 | d2cg4a1 |
| not modelled | 94.7 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
110 | c1bdhA_ |
| not modelled | 94.6 | 31 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (purine repressor); PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
111 | d1jgsa_ |
| not modelled | 94.6 | 12 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
112 | c2qwwB_ |
| not modelled | 94.6 | 17 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution
113 | d2jioa2 |
| not modelled | 94.6 | 14 | Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3
114 | d1stza1 |
| not modelled | 94.5 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain
115 | d2cfxa1 |
| not modelled | 94.5 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
116 | c3lsgD_ |
| not modelled | 94.5 | 10 | 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
117 | c3k2zA_ |
| not modelled | 94.5 | 20 | PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima
118 | c1bl0A_ |
| not modelled | 94.5 | 12 | PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
119 | d1trra_ |
| not modelled | 94.5 | 23 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
120 | c3ecoB_ |
| not modelled | 94.4 | 12 | PDB header:transcription Chain: B: PDB Molecule:mepr; PDBTitle: crystal structure of mepr, a transcription regulator of the2 staphylococcus aureus multidrug efflux pump mepa

Binding site prediction |

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
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Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0