Phyre 2 Results for P33012

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Email | l.a.kelley@imperial.ac.uk
Description | P33012
Date | Thu Jan 5 11:50:47 GMT 2012
Unique Job ID | 37b67fac81212a9d

Summary |

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

Model (left) based on template d1jyha_
Top template information
Fold:Probable bacterial effector-binding domain Superfamily:Probable bacterial effector-binding domain Family:Gyrase inhibitory protein GyrI (SbmC, YeeB)
Confidence and coverage
Confidence: | 100.0% | Coverage: | 99%
155 residues ( 99% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | N | Y | E | I | K | Q | E | E | K | R | T | V | A | G | F | H | L | V | G | P | W | E | Q | T | V | K | K | G | F | E | Q | L | M | M | W | V | D | S | K | N | I | V | P | K | E | W | V | A | V | Y | Y | D | N | P | D | E | T | P | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | E | K | L | R | C | D | T | V | V | T | V | P | G | Y | F | T | L | P | E | N | S | E | G | V | I | L | T | E | I | T | G | G | Q | Y | A | V | A | V | A | R | V | V | G | D | D | F | A | K | P | W | Y | Q | F | F | N | S | L | L | Q | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | .
Sequence |  | S | A | Y | E | M | L | P | K | P | C | F | E | V | Y | L | N | N | G | A | E | D | G | Y | W | D | I | E | M | Y | V | A | V | Q | P | K | H | H
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 |
| d1jyha_ |

### PDB 1jyh chain A

Region: 1 - 155
Aligned: 155
Modelled: 155
Confidence: 100.0%
Identity: 100%
Fold: Probable bacterial effector-binding domain
Superfamily: Probable bacterial effector-binding domain
Family: Gyrase inhibitory protein GyrI (SbmC, YeeB)

Phyre2
2 |
| c3lurB_ |

### PDB 3lur chain B

Region: 1 - 153
Aligned: 149
Modelled: 152
Confidence: 100.0%
Identity: 13%
PDB header:transcription activator
Chain: B: PDB Molecule:putative bacterial transcription regulation protein;
PDBTitle: crystal structure of putative bacterial transcription regulation2 protein (np_372959.1) from staphylococcus aureus mu50 at 1.81 a3 resolution

Phyre2
3 |
| d1d5ya3 |

### PDB 1d5y chain A domain 3

Region: 1 - 155
Aligned: 154
Modelled: 155
Confidence: 100.0%
Identity: 8%
Fold: Probable bacterial effector-binding domain
Superfamily: Probable bacterial effector-binding domain
Family: Rob transcription factor, C-terminal domain

Phyre2
4 |
| c1d5yD_ |

### PDB 1d5y chain D

Region: 1 - 155
Aligned: 154
Modelled: 155
Confidence: 100.0%
Identity: 8%
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
5 |
| c3gk6A_ |

### PDB 3gk6 chain A

Region: 1 - 153
Aligned: 140
Modelled: 150
Confidence: 100.0%
Identity: 16%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:integron cassette protein vch_cass2;
PDBTitle: crystal structure from the mobile metagenome of vibrio cholerae.2 integron cassette protein vch_cass2.

Phyre2
6 |
| c2kcuA_ |

### PDB 2kcu chain A

Region: 1 - 154
Aligned: 146
Modelled: 154
Confidence: 100.0%
Identity: 12%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:protein ctr107;
PDBTitle: nmr solution structure of an uncharacterized protein from2 chlorobium tepidum. northeast structural genomics target3 ctr107

Phyre2
7 |
| c3b49A_ |

### PDB 3b49 chain A

Region: 2 - 152
Aligned: 150
Modelled: 151
Confidence: 99.9%
Identity: 10%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2189 protein;
PDBTitle: crystal structure of an uncharacterized conserved protein from2 listeria innocua

Phyre2
8 |
| d1r8ea2 |

### PDB 1r8e chain A domain 2

Region: 2 - 152
Aligned: 149
Modelled: 151
Confidence: 99.8%
Identity: 11%
Fold: Probable bacterial effector-binding domain
Superfamily: Probable bacterial effector-binding domain
Family: Multidrug-binding domain of transcription activator BmrR

Phyre2
9 |
| c3d6zA_ |

### PDB 3d6z chain A

Region: 2 - 153
Aligned: 150
Modelled: 152
Confidence: 99.7%
Identity: 11%
PDB header:transcription regulator/dna
Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator;
PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine

Phyre2
10 |
| c3r8kB_ |

### PDB 3r8k chain B

Region: 2 - 153
Aligned: 150
Modelled: 152
Confidence: 97.8%
Identity: 15%
PDB header:apoptosis
Chain: B: PDB Molecule:heme-binding protein 2;
PDBTitle: crystal structure of human soul protein (hexagonal form)

Phyre2
11 |
| d2gova1 |

### PDB 2gov chain A domain 1

Region: 2 - 150
Aligned: 147
Modelled: 149
Confidence: 97.7%
Identity: 14%
Fold: Probable bacterial effector-binding domain
Superfamily: Probable bacterial effector-binding domain
Family: SOUL heme-binding protein

Phyre2
12 |
| c2z51A_ |

### PDB 2z51 chain A

Region: 2 - 120
Aligned: 116
Modelled: 119
Confidence: 10.8%
Identity: 11%
PDB header:metal transport
Chain: A: PDB Molecule:nifu-like protein 2, chloroplast;
PDBTitle: crystal structure of arabidopsis cnfu involved in iron-2 sulfur cluster biosynthesis

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1jyha_ |
|  | 100.0 | 100 | Fold:Probable bacterial effector-binding domain Superfamily:Probable bacterial effector-binding domain Family:Gyrase inhibitory protein GyrI (SbmC, YeeB)
2 | c3lurB_ |
|  | 100.0 | 13 | PDB header:transcription activator Chain: B: PDB Molecule:putative bacterial transcription regulation protein; PDBTitle: crystal structure of putative bacterial transcription regulation2 protein (np_372959.1) from staphylococcus aureus mu50 at 1.81 a3 resolution
3 | d1d5ya3 |
|  | 100.0 | 8 | Fold:Probable bacterial effector-binding domain Superfamily:Probable bacterial effector-binding domain Family:Rob transcription factor, C-terminal domain
4 | c1d5yD_ |
|  | 100.0 | 8 | 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
5 | c3gk6A_ |
|  | 100.0 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:integron cassette protein vch_cass2; PDBTitle: crystal structure from the mobile metagenome of vibrio cholerae.2 integron cassette protein vch_cass2.
6 | c2kcuA_ |
|  | 100.0 | 12 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein ctr107; PDBTitle: nmr solution structure of an uncharacterized protein from2 chlorobium tepidum. northeast structural genomics target3 ctr107
7 | c3b49A_ |
|  | 99.9 | 10 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2189 protein; PDBTitle: crystal structure of an uncharacterized conserved protein from2 listeria innocua
8 | d1r8ea2 |
|  | 99.8 | 11 | Fold:Probable bacterial effector-binding domain Superfamily:Probable bacterial effector-binding domain Family:Multidrug-binding domain of transcription activator BmrR
9 | c3d6zA_ |
|  | 99.7 | 11 | PDB header:transcription regulator/dna Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator; PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine
10 | c3r8kB_ |
|  | 97.8 | 15 | PDB header:apoptosis Chain: B: PDB Molecule:heme-binding protein 2; PDBTitle: crystal structure of human soul protein (hexagonal form)
11 | d2gova1 |
|  | 97.7 | 14 | Fold:Probable bacterial effector-binding domain Superfamily:Probable bacterial effector-binding domain Family:SOUL heme-binding protein
12 | c2z51A_ |
|  | 10.8 | 11 | PDB header:metal transport Chain: A: PDB Molecule:nifu-like protein 2, chloroplast; PDBTitle: crystal structure of arabidopsis cnfu involved in iron-2 sulfur cluster biosynthesis

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