Phyre 2 Results for P0A742

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Email | l.a.kelley@imperial.ac.uk
Description | P0A742
Date | Thu Jan 5 11:04:44 GMT 2012
Unique Job ID | c57ae061ff625d82

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2oarA_
Top template information
PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl)
Confidence and coverage
Confidence: | 100.0% | Coverage: | 91%
124 residues ( 91% 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 |

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Sequence |  | M | S | I | I | K | E | F | R | E | F | A | M | R | G | N | V | V | D | L | A | V | G | V | I | I | G | A | A | F | G | K | I | V | S | S | L | V | A | D | I | I | M | P | P | L | G | L | L | I | G | G | I | D | F | K | Q | F | A | V | T
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | L | R | D | A | Q | G | D | I | P | A | V | V | M | H | Y | G | V | F | I | Q | N | V | F | D | F | L | I | V | A | F | A | I | F | M | A | I | K | L | I | N | K | L | N | R | K | K | E | E | P | A | A | A | P | A | P | T | K | E | E | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | .
Sequence |  | L | L | T | E | I | R | D | L | L | K | E | Q | N | N | R | 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 |
| c2oarA_ |

### PDB 2oar chain A

Region: 3 - 133
Aligned: 124
Modelled: 124
Confidence: 100.0%
Identity: 36%
PDB header:membrane protein
Chain: A: PDB Molecule:large-conductance mechanosensitive channel;
PDBTitle: mechanosensitive channel of large conductance (mscl)

Phyre2
2 |
| d2oara1 |

### PDB 2oar chain A domain 1

Region: 12 - 126
Aligned: 108
Modelled: 115
Confidence: 100.0%
Identity: 33%
Fold: Gated mechanosensitive channel
Superfamily: Gated mechanosensitive channel
Family: Gated mechanosensitive channel

Phyre2
3 |
| c3hzqA_ |

### PDB 3hzq chain A

Region: 3 - 106
Aligned: 94
Modelled: 104
Confidence: 100.0%
Identity: 50%
PDB header:membrane protein
Chain: A: PDB Molecule:large-conductance mechanosensitive channel;
PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state

Phyre2
4 |
| c3qnqD_ |

### PDB 3qnq chain D

Region: 32 - 114
Aligned: 83
Modelled: 83
Confidence: 82.2%
Identity: 14%
PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system

Phyre2
5 |
| d1q1va_ |

### PDB 1q1v chain A

Region: 109 - 133
Aligned: 25
Modelled: 25
Confidence: 35.3%
Identity: 28%
Fold: Another 3-helical bundle
Superfamily: DEK C-terminal domain
Family: DEK C-terminal domain

Phyre2
6 |
| c1vdfB_ |

### PDB 1vdf chain B

Region: 120 - 132
Aligned: 13
Modelled: 13
Confidence: 25.8%
Identity: 38%
PDB header:extracellular matrix protein
Chain: B: PDB Molecule:cartilage oligomeric matrix protein;
PDBTitle: assembly domain of cartilage oligomeric matrix protein

Phyre2
7 |
| c3t98A_ |

### PDB 3t98 chain A

Region: 118 - 134
Aligned: 17
Modelled: 17
Confidence: 18.9%
Identity: 41%
PDB header:protein transport
Chain: A: PDB Molecule:nuclear pore complex protein nup54;
PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup54/nup58

Phyre2
8 |
| d1lm8v_ |

### PDB 1lm8 chain V

Region: 113 - 133
Aligned: 21
Modelled: 21
Confidence: 17.8%
Identity: 38%
Fold: Prealbumin-like
Superfamily: VHL
Family: VHL

Phyre2
9 |
| c3n53B_ |

### PDB 3n53 chain B

Region: 114 - 133
Aligned: 20
Modelled: 20
Confidence: 13.9%
Identity: 35%
PDB header:transcription
Chain: B: PDB Molecule:response regulator receiver modulated diguanylate cyclase;
PDBTitle: crystal structure of a response regulator receiver modulated2 diguanylate cyclase from pelobacter carbinolicus

Phyre2
10 |
| d1sh0a_ |

### PDB 1sh0 chain A

Region: 26 - 42
Aligned: 17
Modelled: 17
Confidence: 12.6%
Identity: 12%
Fold: DNA/RNA polymerases
Superfamily: DNA/RNA polymerases
Family: RNA-dependent RNA-polymerase

Phyre2
11 |
| c2uutA_ |

### PDB 2uut chain A

Region: 26 - 42
Aligned: 17
Modelled: 17
Confidence: 11.5%
Identity: 29%
PDB header:hydrolase
Chain: A: PDB Molecule:rna-directed rna polymerase;
PDBTitle: the 2.4 angstrom resolution structure of the d346g mutant2 of the sapporo virus rdrp polymerase

Phyre2
12 |
| c2qzjC_ |

### PDB 2qzj chain C

Region: 113 - 134
Aligned: 22
Modelled: 22
Confidence: 11.4%
Identity: 23%
PDB header:transcription
Chain: C: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of a two-component response regulator from2 clostridium difficile

Phyre2
13 |
| c3snxB_ |

### PDB 3snx chain B

Region: 95 - 132
Aligned: 38
Modelled: 36
Confidence: 10.7%
Identity: 16%
PDB header:sugar binding protein
Chain: B: PDB Molecule:putative susd-like carbohydrate binding protein;
PDBTitle: crystal structure of a putative susd-like carbohydrate binding protein2 (bt_1439) from bacteroides thetaiotaomicron vpi-5482 at 1.88 a3 resolution

Phyre2
14 |
| c1eysH_ |

### PDB 1eys chain H

Region: 82 - 117
Aligned: 36
Modelled: 36
Confidence: 10.6%
Identity: 19%
PDB header:electron transport
Chain: H: PDB Molecule:photosynthetic reaction center;
PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum

Phyre2
15 |
| c2b43D_ |

### PDB 2b43 chain D

Region: 26 - 42
Aligned: 17
Modelled: 17
Confidence: 10.5%
Identity: 12%
PDB header:viral protein
Chain: D: PDB Molecule:non-structural polyprotein;
PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge

Phyre2
16 |
| c2rddB_ |

### PDB 2rdd chain B

Region: 79 - 109
Aligned: 31
Modelled: 31
Confidence: 9.8%
Identity: 6%
PDB header:membrane protein/transport protein
Chain: B: PDB Molecule:upf0092 membrane protein yajc;
PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.

Phyre2
17 |
| d1khva_ |

### PDB 1khv chain A

Region: 26 - 42
Aligned: 17
Modelled: 17
Confidence: 9.1%
Identity: 18%
Fold: DNA/RNA polymerases
Superfamily: DNA/RNA polymerases
Family: RNA-dependent RNA-polymerase

Phyre2
18 |
| c2l35B_ |

### PDB 2l35 chain B

Region: 76 - 95
Aligned: 20
Modelled: 20
Confidence: 8.4%
Identity: 15%
PDB header:protein binding
Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein;
PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer

Phyre2
19 |
| c2l34B_ |

### PDB 2l34 chain B

Region: 76 - 95
Aligned: 20
Modelled: 20
Confidence: 8.0%
Identity: 15%
PDB header:protein binding
Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein;
PDBTitle: structure of the dap12 transmembrane homodimer

Phyre2
20 |
| c2l34A_ |

### PDB 2l34 chain A

Region: 76 - 95
Aligned: 20
Modelled: 20
Confidence: 8.0%
Identity: 15%
PDB header:protein binding
Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein;
PDBTitle: structure of the dap12 transmembrane homodimer

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2oarA_ |
|  | 100.0 | 36 | PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl)
2 | d2oara1 |
|  | 100.0 | 33 | Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel
3 | c3hzqA_ |
|  | 100.0 | 50 | PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state
4 | c3qnqD_ |
|  | 82.2 | 14 | PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system
5 | d1q1va_ |
|  | 35.3 | 28 | Fold:Another 3-helical bundle Superfamily:DEK C-terminal domain Family:DEK C-terminal domain
6 | c1vdfB_ |
|  | 25.8 | 38 | PDB header:extracellular matrix protein Chain: B: PDB Molecule:cartilage oligomeric matrix protein; PDBTitle: assembly domain of cartilage oligomeric matrix protein
7 | c3t98A_ |
|  | 18.9 | 41 | PDB header:protein transport Chain: A: PDB Molecule:nuclear pore complex protein nup54; PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup54/nup58
8 | d1lm8v_ |
|  | 17.8 | 38 | Fold:Prealbumin-like Superfamily:VHL Family:VHL
9 | c3n53B_ |
|  | 13.9 | 35 | PDB header:transcription Chain: B: PDB Molecule:response regulator receiver modulated diguanylate cyclase; PDBTitle: crystal structure of a response regulator receiver modulated2 diguanylate cyclase from pelobacter carbinolicus
10 | d1sh0a_ |
|  | 12.6 | 12 | Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase
11 | c2uutA_ |
|  | 11.5 | 29 | PDB header:hydrolase Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: the 2.4 angstrom resolution structure of the d346g mutant2 of the sapporo virus rdrp polymerase
12 | c2qzjC_ |
|  | 11.4 | 23 | PDB header:transcription Chain: C: PDB Molecule:two-component response regulator; PDBTitle: crystal structure of a two-component response regulator from2 clostridium difficile
13 | c3snxB_ |
|  | 10.7 | 16 | PDB header:sugar binding protein Chain: B: PDB Molecule:putative susd-like carbohydrate binding protein; PDBTitle: crystal structure of a putative susd-like carbohydrate binding protein2 (bt_1439) from bacteroides thetaiotaomicron vpi-5482 at 1.88 a3 resolution
14 | c1eysH_ |
|  | 10.6 | 19 | PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum
15 | c2b43D_ |
|  | 10.5 | 12 | PDB header:viral protein Chain: D: PDB Molecule:non-structural polyprotein; PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge
16 | c2rddB_ |
|  | 9.8 | 6 | PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.
17 | d1khva_ |
|  | 9.1 | 18 | Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase
18 | c2l35B_ |
|  | 8.4 | 15 | PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer
19 | c2l34B_ |
|  | 8.0 | 15 | PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer
20 | c2l34A_ |
|  | 8.0 | 15 | PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer
21 | c3p5nA_ |
| not modelled | 7.4 | 18 | PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter
22 | c2jo1A_ |
| not modelled | 6.6 | 26 | PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles
23 | c3nahC_ |
| not modelled | 6.5 | 24 | PDB header:transferase Chain: C: PDB Molecule:rna dependent rna polymerase; PDBTitle: crystal structures and functional analysis of murine norovirus rna-2 dependent rna polymerase
24 | c2jp3A_ |
| not modelled | 6.4 | 16 | PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles
25 | d1xr6a_ |
| not modelled | 6.2 | 24 | Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase
26 | c1c94B_ |
| not modelled | 6.1 | 36 | PDB header:gene regulation Chain: B: PDB Molecule:retro-gcn4 leucine zipper; PDBTitle: reversing the sequence of the gcn4 leucine zipper does not2 affect its fold.
27 | d2b3wa1 |
| not modelled | 6.0 | 38 | Fold:YbiA-like Superfamily:YbiA-like Family:YbiA-like
28 | d1u09a_ |
| not modelled | 5.8 | 18 | Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase
29 | c3si5X_ |
| not modelled | 5.8 | 38 | PDB header:cell cycle Chain: X: PDB Molecule:protein casc5; PDBTitle: kinetochore-bubr1 kinase complex
30 | c2ijd1_ |
| not modelled | 5.6 | 24 | PDB header:hydrolase, transferase Chain: 1: PDB Molecule:picornain 3c, rna-directed rna polymerase; PDBTitle: crystal structure of the poliovirus precursor protein 3cd
31 | d1xdpa1 |
| not modelled | 5.5 | 14 | Fold:Spectrin repeat-like Superfamily:PPK N-terminal domain-like Family:PPK N-terminal domain-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]
© 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