Phyre 2 Results for P77368

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Email | l.a.kelley@imperial.ac.uk
Description | P77368
Date | Thu Jan 5 12:28:15 GMT 2012
Unique Job ID | a72618a874ccc3c5

Summary |

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

Model (left) based on template d1fuxa_
Top template information
Fold:PEBP-like Superfamily:PEBP-like Family:Prokaryotic PEBP-like proteins
Confidence and coverage
Confidence: | 100.0% | Coverage: | 89%
163 residues ( 89% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | K | T | L | I | V | S | T | V | L | A | F | I | T | F | S | A | Q | A | A | A | F | Q | V | T | S | N | E | I | K | T | G | E | Q | L | T | T | S | H | V | F | S | G | F | G | C | E | G | G | N | T | S | P | S | L | T | W | S | G | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | P | E | G | T | K | S | F | A | V | T | V | Y | D | P | D | A | P | T | G | S | G | W | W | H | W | T | V | V | N | I | P | A | T | V | T | Y | L | P | V | D | A | G | R | R | D | G | T | K | L | P | T | G | A | V | Q | G | R | N | D | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | G | Y | A | G | F | G | G | A | C | P | P | K | G | D | K | P | H | H | Y | Q | F | K | V | W | A | L | K | T | E | K | I | P | V | D | S | N | S | S | G | A | L | V | G | Y | M | L | N | A | N | K | I | A | T | A | E | I | T | P | V | Y
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | .
Sequence |  | E | I | 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 |
| d1fuxa_ |

### PDB 1fux chain A

Region: 21 - 183
Aligned: 163
Modelled: 163
Confidence: 100.0%
Identity: 99%
Fold: PEBP-like
Superfamily: PEBP-like
Family: Prokaryotic PEBP-like proteins

Phyre2
2 |
| d1fjja_ |

### PDB 1fjj chain A

Region: 21 - 180
Aligned: 158
Modelled: 158
Confidence: 100.0%
Identity: 51%
Fold: PEBP-like
Superfamily: PEBP-like
Family: Prokaryotic PEBP-like proteins

Phyre2
3 |
| c3n08A_ |

### PDB 3n08 chain A

Region: 21 - 182
Aligned: 146
Modelled: 157
Confidence: 100.0%
Identity: 36%
PDB header:phosphatidylethanolamine-binding protein
Chain: A: PDB Molecule:putative phosphatidylethanolamine-binding protein (pebp);
PDBTitle: crystal structure of a putative phosphatidylethanolamine-binding2 protein (pebp) homolog ct736 from chlamydia trachomatis d/uw-3/cx

Phyre2
4 |
| c2evvD_ |

### PDB 2evv chain D

Region: 21 - 182
Aligned: 153
Modelled: 157
Confidence: 100.0%
Identity: 27%
PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:hypothetical protein hp0218;
PDBTitle: crystal structure of the pebp-like protein of unknown function hp02182 from helicobacter pylori

Phyre2
5 |
| c2r77A_ |

### PDB 2r77 chain A

Region: 26 - 145
Aligned: 104
Modelled: 104
Confidence: 99.8%
Identity: 24%
PDB header:lipid binding protein
Chain: A: PDB Molecule:phosphatidylethanolamine-binding protein, putative;
PDBTitle: crystal structure of phosphatidylethanolamine-binding protein,2 pfl0955c, from plasmodium falciparum

Phyre2
6 |
| d1wpxb1 |

### PDB 1wpx chain B domain 1

Region: 29 - 180
Aligned: 128
Modelled: 140
Confidence: 99.8%
Identity: 22%
Fold: PEBP-like
Superfamily: PEBP-like
Family: Phosphatidylethanolamine binding protein

Phyre2
7 |
| c2gzqA_ |

### PDB 2gzq chain A

Region: 21 - 156
Aligned: 112
Modelled: 118
Confidence: 99.8%
Identity: 23%
PDB header:lipid binding protein
Chain: A: PDB Molecule:phosphatidylethanolamine-binding protein;
PDBTitle: phosphatidylethanolamine-binding protein from plasmodium vivax

Phyre2
8 |
| c2jyzA_ |

### PDB 2jyz chain A

Region: 12 - 158
Aligned: 118
Modelled: 128
Confidence: 99.8%
Identity: 30%
PDB header:unknown function
Chain: A: PDB Molecule:cg7054-pa;
PDBTitle: cg7054 solution structure

Phyre2
9 |
| c1wkpA_ |

### PDB 1wkp chain A

Region: 17 - 183
Aligned: 134
Modelled: 154
Confidence: 99.7%
Identity: 22%
PDB header:signaling protein
Chain: A: PDB Molecule:flowering locus t protein;
PDBTitle: flowering locus t (ft) from arabidopsis thaliana

Phyre2
10 |
| d1kn3a_ |

### PDB 1kn3 chain A

Region: 16 - 155
Aligned: 109
Modelled: 119
Confidence: 99.7%
Identity: 28%
Fold: PEBP-like
Superfamily: PEBP-like
Family: Phosphatidylethanolamine binding protein

Phyre2
11 |
| d2qyqa1 |

### PDB 2qyq chain A domain 1

Region: 13 - 155
Aligned: 112
Modelled: 129
Confidence: 99.7%
Identity: 29%
Fold: PEBP-like
Superfamily: PEBP-like
Family: Phosphatidylethanolamine binding protein

Phyre2
12 |
| d1a44a_ |

### PDB 1a44 chain A

Region: 53 - 155
Aligned: 81
Modelled: 82
Confidence: 99.7%
Identity: 26%
Fold: PEBP-like
Superfamily: PEBP-like
Family: Phosphatidylethanolamine binding protein

Phyre2
13 |
| d1qoua_ |

### PDB 1qou chain A

Region: 29 - 165
Aligned: 105
Modelled: 115
Confidence: 99.7%
Identity: 20%
Fold: PEBP-like
Superfamily: PEBP-like
Family: Phosphatidylethanolamine binding protein

Phyre2
14 |
| c3ks7D_ |

### PDB 3ks7 chain D

Region: 46 - 87
Aligned: 42
Modelled: 42
Confidence: 45.6%
Identity: 26%
PDB header:hydrolase
Chain: D: PDB Molecule:putative putative pngase f;
PDBTitle: crystal structure of putative peptide:n-glycosidase f (pngase f)2 (yp_210507.1) from bacteroides fragilis nctc 9343 at 2.30 a3 resolution

Phyre2
15 |
| d1qcsa1 |

### PDB 1qcs chain A domain 1

Region: 103 - 143
Aligned: 38
Modelled: 41
Confidence: 11.1%
Identity: 21%
Fold: Double psi beta-barrel
Superfamily: ADC-like
Family: Cdc48 N-terminal domain-like

Phyre2
16 |
| c1ljzB_ |

### PDB 1ljz chain B

Region: 80 - 97
Aligned: 18
Modelled: 18
Confidence: 10.7%
Identity: 33%
PDB header:receptor, toxin
Chain: B: PDB Molecule:acetylcholine receptor protein;
PDBTitle: nmr structure of an achr-peptide (torpedo californica,2 alpha-subunit residues 182-202) in complex with alpha-3 bungarotoxin

Phyre2
17 |
| c3pnrB_ |

### PDB 3pnr chain B

Region: 69 - 90
Aligned: 21
Modelled: 22
Confidence: 9.9%
Identity: 24%
PDB header:hydrolase/hydrolase inhibitor
Chain: B: PDB Molecule:pbicp-c;
PDBTitle: structure of pbicp-c in complex with falcipain-2

Phyre2
18 |
| c3kmlB_ |

### PDB 3kml chain B

Region: 55 - 70
Aligned: 16
Modelled: 16
Confidence: 7.2%
Identity: 38%
PDB header:viral protein
Chain: B: PDB Molecule:coat protein;
PDBTitle: circular permutant of the tobacco mosaic virus

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1fuxa_ |
|  | 100.0 | 99 | Fold:PEBP-like Superfamily:PEBP-like Family:Prokaryotic PEBP-like proteins
2 | d1fjja_ |
|  | 100.0 | 51 | Fold:PEBP-like Superfamily:PEBP-like Family:Prokaryotic PEBP-like proteins
3 | c3n08A_ |
|  | 100.0 | 36 | PDB header:phosphatidylethanolamine-binding protein Chain: A: PDB Molecule:putative phosphatidylethanolamine-binding protein (pebp); PDBTitle: crystal structure of a putative phosphatidylethanolamine-binding2 protein (pebp) homolog ct736 from chlamydia trachomatis d/uw-3/cx
4 | c2evvD_ |
|  | 100.0 | 27 | PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein hp0218; PDBTitle: crystal structure of the pebp-like protein of unknown function hp02182 from helicobacter pylori
5 | c2r77A_ |
|  | 99.8 | 24 | PDB header:lipid binding protein Chain: A: PDB Molecule:phosphatidylethanolamine-binding protein, putative; PDBTitle: crystal structure of phosphatidylethanolamine-binding protein,2 pfl0955c, from plasmodium falciparum
6 | d1wpxb1 |
|  | 99.8 | 22 | Fold:PEBP-like Superfamily:PEBP-like Family:Phosphatidylethanolamine binding protein
7 | c2gzqA_ |
|  | 99.8 | 23 | PDB header:lipid binding protein Chain: A: PDB Molecule:phosphatidylethanolamine-binding protein; PDBTitle: phosphatidylethanolamine-binding protein from plasmodium vivax
8 | c2jyzA_ |
|  | 99.8 | 30 | PDB header:unknown function Chain: A: PDB Molecule:cg7054-pa; PDBTitle: cg7054 solution structure
9 | c1wkpA_ |
|  | 99.7 | 22 | PDB header:signaling protein Chain: A: PDB Molecule:flowering locus t protein; PDBTitle: flowering locus t (ft) from arabidopsis thaliana
10 | d1kn3a_ |
|  | 99.7 | 28 | Fold:PEBP-like Superfamily:PEBP-like Family:Phosphatidylethanolamine binding protein
11 | d2qyqa1 |
|  | 99.7 | 29 | Fold:PEBP-like Superfamily:PEBP-like Family:Phosphatidylethanolamine binding protein
12 | d1a44a_ |
|  | 99.7 | 26 | Fold:PEBP-like Superfamily:PEBP-like Family:Phosphatidylethanolamine binding protein
13 | d1qoua_ |
|  | 99.7 | 20 | Fold:PEBP-like Superfamily:PEBP-like Family:Phosphatidylethanolamine binding protein
14 | c3ks7D_ |
|  | 45.6 | 26 | PDB header:hydrolase Chain: D: PDB Molecule:putative putative pngase f; PDBTitle: crystal structure of putative peptide:n-glycosidase f (pngase f)2 (yp_210507.1) from bacteroides fragilis nctc 9343 at 2.30 a3 resolution
15 | d1qcsa1 |
|  | 11.1 | 21 | Fold:Double psi beta-barrel Superfamily:ADC-like Family:Cdc48 N-terminal domain-like
16 | c1ljzB_ |
|  | 10.7 | 33 | PDB header:receptor, toxin Chain: B: PDB Molecule:acetylcholine receptor protein; PDBTitle: nmr structure of an achr-peptide (torpedo californica,2 alpha-subunit residues 182-202) in complex with alpha-3 bungarotoxin
17 | c3pnrB_ |
|  | 9.9 | 24 | PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:pbicp-c; PDBTitle: structure of pbicp-c in complex with falcipain-2
18 | c3kmlB_ |
|  | 7.2 | 38 | PDB header:viral protein Chain: B: PDB Molecule:coat protein; PDBTitle: circular permutant of the tobacco mosaic virus

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