Phyre 2 Results for Q46896

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Email | l.a.kelley@imperial.ac.uk
Description | Q46896
Date | Thu Jan 5 12:35:36 GMT 2012
Unique Job ID | be002e84e4cf9d7f

Summary |

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

Model (left) based on template c3nkdB_
Top template information
PDB header:immune system Chain: B: PDB Molecule:crispr-associated protein cas1; PDBTitle: structure of crisp-associated protein cas1 from escherichia coli str.2 k-12
Confidence and coverage
Confidence: | 100.0% | Coverage: | 86%
261 residues ( 86% 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 | T | W | L | P | L | N | P | I | P | L | K | D | R | V | S | M | I | F | L | Q | Y | G | Q | I | D | V | I | D | G | A | F | V | L | I | D | K | T | G | I | R | T | H | I | P | V | G | S | V | A | C | I | M | L | E | P | G | T | R | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | H | A | A | V | R | L | A | A | Q | V | G | T | L | L | V | W | V | G | E | A | G | V | R | V | Y | A | S | G | Q | P | G | G | A | R | S | D | K | L | L | Y | Q | A | K | L | A | L | D | E | D | L | R | L | K | V | V | R | K | M | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | E | L | R | F | G | E | P | A | P | A | R | R | S | V | E | Q | L | R | G | I | E | G | S | R | V | R | A | T | Y | A | L | L | A | K | Q | Y | G | V | T | W | N | G | R | R | Y | D | P | K | D | W | E | K | G | D | T | I | N | Q | C | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | S | A | A | T | S | C | L | Y | G | V | T | E | A | A | I | L | A | A | G | Y | A | P | A | I | G | F | V | H | T | G | K | P | L | S | F | V | Y | D | I | A | D | I | I | K | F | D | T | V | V | P | K | A | F | E | I | A | R | R | N | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | G | E | P | D | R | E | V | R | L | A | C | R | D | I | F | R | S | S | K | T | L | A | K | L | I | P | L | I | E | D | V | L | A | A | G | E | I | Q | P | P | A | P | P | E | D | A | Q | P | V | A | I | P | L | P | V | S | L | G | D | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | .
Sequence |  | G | H | R | S | S
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 |
| c3nkdB_ |

### PDB 3nkd chain B

Region: 9 - 280
Aligned: 261
Modelled: 272
Confidence: 100.0%
Identity: 99%
PDB header:immune system
Chain: B: PDB Molecule:crispr-associated protein cas1;
PDBTitle: structure of crisp-associated protein cas1 from escherichia coli str.2 k-12

Phyre2
2 |
| c3godA_ |

### PDB 3god chain A

Region: 5 - 273
Aligned: 264
Modelled: 269
Confidence: 100.0%
Identity: 25%
PDB header:immune system
Chain: A: PDB Molecule:cas1;
PDBTitle: structural basis for dnase activity of a conserved protein2 implicated in crispr-mediated antiviral defense

Phyre2
3 |
| c3lfxE_ |

### PDB 3lfx chain E

Region: 16 - 257
Aligned: 239
Modelled: 242
Confidence: 100.0%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: E: PDB Molecule:uncharacterized protein;
PDBTitle: structure of tm1797, a cas1 protein from thermotoga maritima

Phyre2
4 |
| c2yzsB_ |

### PDB 2yzs chain B

Region: 18 - 257
Aligned: 233
Modelled: 240
Confidence: 100.0%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of uncharacterized conserved protein from2 aquifex aeolicus

Phyre2
5 |
| c3pv9D_ |

### PDB 3pv9 chain D

Region: 14 - 244
Aligned: 215
Modelled: 216
Confidence: 100.0%
Identity: 17%
PDB header:immune system
Chain: D: PDB Molecule:putative uncharacterized protein ph1245;
PDBTitle: structure of ph1245, a cas1 from pyrococcus horikoshii

Phyre2
6 |
| c3nkeA_ |

### PDB 3nke chain A

Region: 96 - 280
Aligned: 181
Modelled: 185
Confidence: 100.0%
Identity: 99%
PDB header:immune system
Chain: A: PDB Molecule:protein ygbt;
PDBTitle: high resolution structure of the c-terminal domain crisp-associated2 protein cas1 from escherichia coli str. k-12

Phyre2
7 |
| d1p3da1 |

### PDB 1p3d chain A domain 1

Region: 46 - 76
Aligned: 31
Modelled: 31
Confidence: 73.8%
Identity: 3%
Fold: MurCD N-terminal domain
Superfamily: MurCD N-terminal domain
Family: MurCD N-terminal domain

Phyre2
8 |
| d2jfga1 |

### PDB 2jfg chain A domain 1

Region: 46 - 76
Aligned: 31
Modelled: 31
Confidence: 71.5%
Identity: 26%
Fold: MurCD N-terminal domain
Superfamily: MurCD N-terminal domain
Family: MurCD N-terminal domain

Phyre2
9 |
| d1j6ua1 |

### PDB 1j6u chain A domain 1

Region: 46 - 76
Aligned: 31
Modelled: 31
Confidence: 63.4%
Identity: 10%
Fold: MurCD N-terminal domain
Superfamily: MurCD N-terminal domain
Family: MurCD N-terminal domain

Phyre2
10 |
| d2ioja1 |

### PDB 2ioj chain A domain 1

Region: 29 - 81
Aligned: 53
Modelled: 53
Confidence: 48.3%
Identity: 13%
Fold: MurF and HprK N-domain-like
Superfamily: HprK N-terminal domain-like
Family: DRTGG domain

Phyre2
11 |
| c1jrxA_ |

### PDB 1jrx chain A

Region: 44 - 81
Aligned: 37
Modelled: 38
Confidence: 42.1%
Identity: 19%
PDB header:oxidoreductase
Chain: A: PDB Molecule:flavocytochrome c;
PDBTitle: crystal structure of arg402ala mutant flavocytochrome c32 from shewanella frigidimarina

Phyre2
12 |
| c3nixF_ |

### PDB 3nix chain F

Region: 49 - 103
Aligned: 54
Modelled: 55
Confidence: 39.1%
Identity: 20%
PDB header:oxidoreductase
Chain: F: PDB Molecule:flavoprotein/dehydrogenase;
PDBTitle: crystal structure of flavoprotein/dehydrogenase from cytophaga2 hutchinsonii. northeast structural genomics consortium target chr43.

Phyre2
13 |
| c2hbpA_ |

### PDB 2hbp chain A

Region: 20 - 50
Aligned: 31
Modelled: 31
Confidence: 37.0%
Identity: 13%
PDB header:endocytosis, protein binding
Chain: A: PDB Molecule:cytoskeleton assembly control protein sla1;
PDBTitle: solution structure of sla1 homology domain 1

Phyre2
14 |
| c3lhlA_ |

### PDB 3lhl chain A

Region: 52 - 81
Aligned: 30
Modelled: 30
Confidence: 33.6%
Identity: 7%
PDB header:hydrolase
Chain: A: PDB Molecule:putative agmatinase;
PDBTitle: crystal structure of a putative agmatinase from clostridium difficile

Phyre2
15 |
| c1qo8A_ |

### PDB 1qo8 chain A

Region: 44 - 81
Aligned: 37
Modelled: 38
Confidence: 33.3%
Identity: 19%
PDB header:oxidoreductase
Chain: A: PDB Molecule:flavocytochrome c3 fumarate reductase;
PDBTitle: the structure of the open conformation of a flavocytochrome2 c3 fumarate reductase

Phyre2
16 |
| c2aczA_ |

### PDB 2acz chain A

Region: 43 - 82
Aligned: 39
Modelled: 40
Confidence: 27.2%
Identity: 18%
PDB header:oxidoreductase/electron transport
Chain: A: PDB Molecule:succinate dehydrogenase flavoprotein subunit;
PDBTitle: complex ii (succinate dehydrogenase) from e. coli with atpenin a52 inhibitor co-crystallized at the ubiquinone binding site

Phyre2
17 |
| c2f00A_ |

### PDB 2f00 chain A

Region: 45 - 76
Aligned: 32
Modelled: 32
Confidence: 26.7%
Identity: 6%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate--l-alanine ligase;
PDBTitle: escherichia coli murc

Phyre2
18 |
| d1woha_ |

### PDB 1woh chain A

Region: 52 - 82
Aligned: 31
Modelled: 31
Confidence: 26.6%
Identity: 19%
Fold: Arginase/deacetylase
Superfamily: Arginase/deacetylase
Family: Arginase-like amidino hydrolases

Phyre2
19 |
| c3mlqH_ |

### PDB 3mlq chain H

Region: 28 - 52
Aligned: 25
Modelled: 25
Confidence: 22.8%
Identity: 20%
PDB header:transferase/transcription
Chain: H: PDB Molecule:transcription-repair coupling factor;
PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain

Phyre2
20 |
| c1yq4A_ |

### PDB 1yq4 chain A

Region: 42 - 82
Aligned: 40
Modelled: 41
Confidence: 21.6%
Identity: 23%
PDB header:oxidoreductase
Chain: A: PDB Molecule:succinate dehydrogenase flavoprotein subunit;
PDBTitle: avian respiratory complex ii with 3-nitropropionate and ubiquinone

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3nkdB_ |
|  | 100.0 | 99 | PDB header:immune system Chain: B: PDB Molecule:crispr-associated protein cas1; PDBTitle: structure of crisp-associated protein cas1 from escherichia coli str.2 k-12
2 | c3godA_ |
|  | 100.0 | 25 | PDB header:immune system Chain: A: PDB Molecule:cas1; PDBTitle: structural basis for dnase activity of a conserved protein2 implicated in crispr-mediated antiviral defense
3 | c3lfxE_ |
|  | 100.0 | 18 | PDB header:structural genomics, unknown function Chain: E: PDB Molecule:uncharacterized protein; PDBTitle: structure of tm1797, a cas1 protein from thermotoga maritima
4 | c2yzsB_ |
|  | 100.0 | 17 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of uncharacterized conserved protein from2 aquifex aeolicus
5 | c3pv9D_ |
|  | 100.0 | 17 | PDB header:immune system Chain: D: PDB Molecule:putative uncharacterized protein ph1245; PDBTitle: structure of ph1245, a cas1 from pyrococcus horikoshii
6 | c3nkeA_ |
|  | 100.0 | 99 | PDB header:immune system Chain: A: PDB Molecule:protein ygbt; PDBTitle: high resolution structure of the c-terminal domain crisp-associated2 protein cas1 from escherichia coli str. k-12
7 | d1p3da1 |
|  | 73.8 | 3 | Fold:MurCD N-terminal domain Superfamily:MurCD N-terminal domain Family:MurCD N-terminal domain
8 | d2jfga1 |
|  | 71.5 | 26 | Fold:MurCD N-terminal domain Superfamily:MurCD N-terminal domain Family:MurCD N-terminal domain
9 | d1j6ua1 |
|  | 63.4 | 10 | Fold:MurCD N-terminal domain Superfamily:MurCD N-terminal domain Family:MurCD N-terminal domain
10 | d2ioja1 |
|  | 48.3 | 13 | Fold:MurF and HprK N-domain-like Superfamily:HprK N-terminal domain-like Family:DRTGG domain
11 | c1jrxA_ |
|  | 42.1 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:flavocytochrome c; PDBTitle: crystal structure of arg402ala mutant flavocytochrome c32 from shewanella frigidimarina
12 | c3nixF_ |
|  | 39.1 | 20 | PDB header:oxidoreductase Chain: F: PDB Molecule:flavoprotein/dehydrogenase; PDBTitle: crystal structure of flavoprotein/dehydrogenase from cytophaga2 hutchinsonii. northeast structural genomics consortium target chr43.
13 | c2hbpA_ |
|  | 37.0 | 13 | PDB header:endocytosis, protein binding Chain: A: PDB Molecule:cytoskeleton assembly control protein sla1; PDBTitle: solution structure of sla1 homology domain 1
14 | c3lhlA_ |
|  | 33.6 | 7 | PDB header:hydrolase Chain: A: PDB Molecule:putative agmatinase; PDBTitle: crystal structure of a putative agmatinase from clostridium difficile
15 | c1qo8A_ |
|  | 33.3 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:flavocytochrome c3 fumarate reductase; PDBTitle: the structure of the open conformation of a flavocytochrome2 c3 fumarate reductase
16 | c2aczA_ |
|  | 27.2 | 18 | PDB header:oxidoreductase/electron transport Chain: A: PDB Molecule:succinate dehydrogenase flavoprotein subunit; PDBTitle: complex ii (succinate dehydrogenase) from e. coli with atpenin a52 inhibitor co-crystallized at the ubiquinone binding site
17 | c2f00A_ |
|  | 26.7 | 6 | PDB header:ligase Chain: A: PDB Molecule:udp-n-acetylmuramate--l-alanine ligase; PDBTitle: escherichia coli murc
18 | d1woha_ |
|  | 26.6 | 19 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
19 | c3mlqH_ |
|  | 22.8 | 20 | PDB header:transferase/transcription Chain: H: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain
20 | c1yq4A_ |
|  | 21.6 | 23 | PDB header:oxidoreductase Chain: A: PDB Molecule:succinate dehydrogenase flavoprotein subunit; PDBTitle: avian respiratory complex ii with 3-nitropropionate and ubiquinone
21 | c3nipB_ |
| not modelled | 20.6 | 10 | PDB header:hydrolase Chain: B: PDB Molecule:3-guanidinopropionase; PDBTitle: crystal structure of pseudomonas aeruginosa guanidinopropionase2 complexed with 1,6-diaminohexane
22 | c3m1rF_ |
| not modelled | 20.1 | 17 | PDB header:hydrolase Chain: F: PDB Molecule:formimidoylglutamase; PDBTitle: the crystal structure of formimidoylglutamase from bacillus2 subtilis subsp. subtilis str. 168
23 | c3ff4A_ |
| not modelled | 19.8 | 8 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of uncharacterized protein chu_1412
24 | d1neka2 |
| not modelled | 19.6 | 18 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain
25 | d2aeba1 |
| not modelled | 19.6 | 13 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
26 | d1xfka_ |
| not modelled | 18.5 | 23 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
27 | d2d59a1 |
| not modelled | 18.5 | 17 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:CoA-binding domain
28 | d1gq6a_ |
| not modelled | 18.4 | 23 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
29 | c1jqoA_ |
| not modelled | 18.3 | 20 | PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxylase; PDBTitle: crystal structure of c4-form phosphoenolpyruvate carboxylase from2 maize
30 | d1jqoa_ |
| not modelled | 18.3 | 20 | Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate carboxylase
31 | d1pq3a_ |
| not modelled | 17.6 | 17 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
32 | d1zhva2 |
| not modelled | 17.2 | 11 | Fold:Ferredoxin-like Superfamily:ACT-like Family:Atu0741-like
33 | c1d4cB_ |
| not modelled | 16.6 | 13 | PDB header:oxidoreductase Chain: B: PDB Molecule:flavocytochrome c fumarate reductase; PDBTitle: crystal structure of the uncomplexed form of the2 flavocytochrome c fumarate reductase of shewanella3 putrefaciens strain mr-1
34 | c2cunA_ |
| not modelled | 16.5 | 13 | PDB header:transferase Chain: A: PDB Molecule:phosphoglycerate kinase; PDBTitle: crystal structure of phosphoglycerate kinase from pyrococcus2 horikoshii ot3
35 | c3bioB_ |
| not modelled | 15.5 | 13 | PDB header:oxidoreductase Chain: B: PDB Molecule:oxidoreductase, gfo/idh/moca family; PDBTitle: crystal structure of oxidoreductase (gfo/idh/moca family member) from2 porphyromonas gingivalis w83
36 | c1j6uA_ |
| not modelled | 15.0 | 9 | PDB header:ligase Chain: A: PDB Molecule:udp-n-acetylmuramate-alanine ligase murc; PDBTitle: crystal structure of udp-n-acetylmuramate-alanine ligase2 murc (tm0231) from thermotoga maritima at 2.3 a resolution
37 | c3ihgA_ |
| not modelled | 15.0 | 21 | PDB header:flavoprotein, oxidoreductase Chain: A: PDB Molecule:rdme; PDBTitle: crystal structure of a ternary complex of aklavinone-112 hydroxylase with fad and aklavinone
38 | c2e1mA_ |
| not modelled | 15.0 | 14 | PDB header:oxidoreductase Chain: A: PDB Molecule:l-glutamate oxidase; PDBTitle: crystal structure of l-glutamate oxidase from streptomyces sp. x-119-6
39 | d2q4qa1 |
| not modelled | 14.3 | 16 | Fold:MTH938-like Superfamily:MTH938-like Family:MTH938-like
40 | d1w4xa1 |
| not modelled | 13.8 | 22 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains
41 | d1cr6a2 |
| not modelled | 13.7 | 16 | Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:Epoxide hydrolase
42 | d2a0ma1 |
| not modelled | 13.3 | 13 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
43 | d1vpea_ |
| not modelled | 13.0 | 15 | Fold:Phosphoglycerate kinase Superfamily:Phosphoglycerate kinase Family:Phosphoglycerate kinase
44 | d1ko7a1 |
| not modelled | 12.9 | 15 | Fold:MurF and HprK N-domain-like Superfamily:HprK N-terminal domain-like Family:HPr kinase/phoshatase HprK N-terminal domain
45 | d2ceva_ |
| not modelled | 12.9 | 13 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
46 | d2ooxe2 |
| not modelled | 12.8 | 14 | Fold:CBS-domain pair Superfamily:CBS-domain pair Family:CBS-domain pair
47 | c3mlqE_ |
| not modelled | 12.8 | 26 | PDB header:transferase/transcription Chain: E: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain
48 | c2eivH_ |
| not modelled | 12.7 | 30 | PDB header:hydrolase Chain: H: PDB Molecule:arginase; PDBTitle: crystal structure of the arginase from thermus thermophilus
49 | d2fvta1 |
| not modelled | 12.6 | 13 | Fold:MTH938-like Superfamily:MTH938-like Family:MTH938-like
50 | c2kbrA_ |
| not modelled | 12.5 | 8 | PDB header:structural protein/cell adhesion Chain: A: PDB Molecule:harmonin; PDBTitle: solution structure of harmonin n terminal domain in complex2 with a internal peptide of cadherin23
51 | d1iuka_ |
| not modelled | 12.5 | 11 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:CoA-binding domain
52 | d1v6sa_ |
| not modelled | 12.5 | 22 | Fold:Phosphoglycerate kinase Superfamily:Phosphoglycerate kinase Family:Phosphoglycerate kinase
53 | c2pd2A_ |
| not modelled | 12.1 | 9 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein st0148; PDBTitle: crystal structure of (st0148) conserved hypothetical from sulfolobus2 tokodaii strain7
54 | d1phpa_ |
| not modelled | 12.1 | 15 | Fold:Phosphoglycerate kinase Superfamily:Phosphoglycerate kinase Family:Phosphoglycerate kinase
55 | d1gsoa2 |
| not modelled | 12.0 | 10 | Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:BC N-terminal domain-like
56 | d1ybha1 |
| not modelled | 12.0 | 9 | Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Pyruvate oxidase and decarboxylase, middle domain
57 | d1zvpa2 |
| not modelled | 11.8 | 13 | Fold:Ferredoxin-like Superfamily:ACT-like Family:VC0802-like
58 | d1zd3a2 |
| not modelled | 11.7 | 19 | Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:Epoxide hydrolase
59 | c3do5A_ |
| not modelled | 11.5 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:homoserine dehydrogenase; PDBTitle: crystal structure of putative homoserine dehydrogenase (np_069768.1)2 from archaeoglobus fulgidus at 2.20 a resolution
60 | d1d3va_ |
| not modelled | 11.3 | 13 | Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Arginase-like amidino hydrolases
61 | c3mmrA_ |
| not modelled | 11.1 | 13 | PDB header:hydrolase Chain: A: PDB Molecule:arginase; PDBTitle: structure of plasmodium falciparum arginase in complex with abh
62 | c3cpiH_ |
| not modelled | 11.1 | 14 | PDB header:protein transport Chain: H: PDB Molecule:rab gdp-dissociation inhibitor; PDBTitle: crystal structure of yeast rab-gdi
63 | c2qa2A_ |
| not modelled | 10.9 | 12 | PDB header:oxidoreductase Chain: A: PDB Molecule:polyketide oxygenase cabe; PDBTitle: crystal structure of cabe, an aromatic hydroxylase from angucycline2 biosynthesis, determined to 2.7 a resolution
64 | c1zmrA_ |
| not modelled | 10.9 | 20 | PDB header:transferase Chain: A: PDB Molecule:phosphoglycerate kinase; PDBTitle: crystal structure of the e. coli phosphoglycerate kinase
65 | c1s1hB_ |
| not modelled | 10.8 | 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.
66 | c2duwA_ |
| not modelled | 10.7 | 11 | PDB header:ligand binding protein Chain: A: PDB Molecule:putative coa-binding protein; PDBTitle: solution structure of putative coa-binding protein of2 klebsiella pneumoniae
67 | d2eyqa1 |
| not modelled | 10.6 | 20 | Fold:SH3-like barrel Superfamily:CarD-like Family:CarD-like
68 | d2gf3a1 |
| not modelled | 10.4 | 18 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD-linked reductases, N-terminal domain
69 | c2dkhA_ |
| not modelled | 10.4 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:3-hydroxybenzoate hydroxylase; PDBTitle: crystal structure of 3-hydroxybenzoate hydroxylase from comamonas2 testosteroni, in complex with the substrate
70 | d2fi9a1 |
| not modelled | 10.2 | 9 | Fold:MTH938-like Superfamily:MTH938-like Family:MTH938-like
71 | c3pzlA_ |
| not modelled | 10.1 | 27 | PDB header:hydrolase Chain: A: PDB Molecule:agmatine ureohydrolase; PDBTitle: the crystal structure of agmatine ureohydrolase of thermoplasma2 volcanium
72 | d2nmla1 |
| not modelled | 10.1 | 24 | Fold:ERH-like Superfamily:ERH-like Family:ERH-like
73 | c3q3vA_ |
| not modelled | 9.8 | 14 | PDB header:transferase Chain: A: PDB Molecule:phosphoglycerate kinase; PDBTitle: crystal structure of phosphoglycerate kinase from campylobacter2 jejuni.
74 | c2r4jA_ |
| not modelled | 9.8 | 17 | PDB header:oxidoreductase Chain: A: PDB Molecule:aerobic glycerol-3-phosphate dehydrogenase; PDBTitle: crystal structure of escherichia coli semet substituted2 glycerol-3-phosphate dehydrogenase in complex with dhap
75 | c3fwzA_ |
| not modelled | 9.7 | 16 | PDB header:membrane protein Chain: A: PDB Molecule:inner membrane protein ybal; PDBTitle: crystal structure of trka-n domain of inner membrane protein ybal from2 escherichia coli
76 | c3nioF_ |
| not modelled | 9.6 | 21 | PDB header:hydrolase Chain: F: PDB Molecule:guanidinobutyrase; PDBTitle: crystal structure of pseudomonas aeruginosa guanidinobutyrase
77 | d1otha2 |
| not modelled | 9.5 | 19 | Fold:ATC-like Superfamily:Aspartate/ornithine carbamoyltransferase Family:Aspartate/ornithine carbamoyltransferase
78 | d2bcgg1 |
| not modelled | 9.2 | 14 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:GDI-like N domain
79 | d1euca1 |
| not modelled | 9.1 | 17 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:CoA-binding domain
80 | c2yg4B_ |
| not modelled | 9.0 | 13 | PDB header:oxidoreductase Chain: B: PDB Molecule:putrescine oxidase; PDBTitle: structure-based redesign of cofactor binding in putrescine2 oxidase: wild type bound to putrescine
81 | c1oy5B_ |
| not modelled | 8.7 | 16 | PDB header:transferase Chain: B: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: crystal structure of trna (m1g37) methyltransferase from aquifex2 aeolicus
82 | d1oy5a_ |
| not modelled | 8.7 | 16 | Fold:alpha/beta knot Superfamily:alpha/beta knot Family:tRNA(m1G37)-methyltransferase TrmD
83 | c3mpoD_ |
| not modelled | 8.7 | 24 | PDB header:hydrolase Chain: D: PDB Molecule:predicted hydrolase of the had superfamily; PDBTitle: the crystal structure of a hydrolase from lactobacillus brevis
84 | c2rgoA_ |
| not modelled | 8.6 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:alpha-glycerophosphate oxidase; PDBTitle: structure of alpha-glycerophosphate oxidase from2 streptococcus sp.: a template for the mitochondrial alpha-3 glycerophosphate dehydrogenase
85 | d1y81a1 |
| not modelled | 8.5 | 17 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:CoA-binding domain
86 | c2p58A_ |
| not modelled | 8.4 | 15 | PDB header:transport protein/chaperone Chain: A: PDB Molecule:putative type iii secretion protein ysce; PDBTitle: structure of the yersinia pestis type iii secretion system2 needle protein yscf in complex with its chaperones3 ysce/yscg
87 | c3fmwC_ |
| not modelled | 8.3 | 9 | PDB header:oxidoreductase Chain: C: PDB Molecule:oxygenase; PDBTitle: the crystal structure of mtmoiv, a baeyer-villiger2 monooxygenase from the mithramycin biosynthetic pathway in3 streptomyces argillaceus.
88 | d2ozga1 |
| not modelled | 8.3 | 13 | Fold:SCP-like Superfamily:SCP-like Family:EF1021 C-terminal domain-like
89 | c3nyeA_ |
| not modelled | 8.3 | 14 | PDB header:oxidoreductase Chain: A: PDB Molecule:d-arginine dehydrogenase; PDBTitle: crystal structure of pseudomonas aeruginosa d-arginine dehydrogenase2 in complex with imino-arginine
90 | d1zcza2 |
| not modelled | 8.2 | 12 | Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC
91 | c1zvpB_ |
| not modelled | 8.1 | 13 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein vc0802; PDBTitle: crystal structure of a protein of unknown function vc0802 from vibrio2 cholerae, possible transport protein
92 | c2l2qA_ |
| not modelled | 8.1 | 15 | PDB header:transferase Chain: A: PDB Molecule:pts system, cellobiose-specific iib component (cela); PDBTitle: solution structure of cellobiose-specific phosphotransferase iib2 component protein from borrelia burgdorferi
93 | d3coxa1 |
| not modelled | 8.1 | 26 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD-linked reductases, N-terminal domain
94 | c2d6fA_ |
| not modelled | 7.9 | 20 | PDB header:ligase/rna Chain: A: PDB Molecule:glutamyl-trna(gln) amidotransferase subunit d; PDBTitle: crystal structure of glu-trna(gln) amidotransferase in the2 complex with trna(gln)
95 | d1rlga_ |
| not modelled | 7.9 | 9 | Fold:Bacillus chorismate mutase-like Superfamily:L30e-like Family:L30e/L7ae ribosomal proteins
96 | d2cvza1 |
| not modelled | 7.8 | 22 | Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain
97 | d2npta1 |
| not modelled | 7.7 | 12 | Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain
98 | c3l78A_ |
| not modelled | 7.6 | 9 | PDB header:transcription Chain: A: PDB Molecule:regulatory protein spx; PDBTitle: the crystal structure of smu.1142c from streptococcus mutans ua159
99 | c3nbmA_ |
| not modelled | 7.5 | 24 | PDB header:transferase Chain: A: PDB Molecule:pts system, lactose-specific iibc components; PDBTitle: the lactose-specific iib component domain structure of the2 phosphoenolpyruvate:carbohydrate phosphotransferase system (pts) from3 streptococcus pneumoniae.

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