Phyre 2 Results for P0ADV1

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P0ADV1
Date | Thu Jan 5 11:21:54 GMT 2012
Unique Job ID | 7e2b64c05d90dac9

Summary |

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

Model (left) based on template c2r1aD_
Top template information
PDB header:transport protein Chain: D: PDB Molecule:protein yhbn; PDBTitle: crystal structure of the periplasmic lipopolysaccharide transport2 protein lpta (yhbn), trigonal form
Confidence and coverage
Confidence: | 100.0% | Coverage: | 74%
136 residues ( 74% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | K | F | K | T | N | K | L | S | L | N | L | V | L | A | S | S | L | L | A | A | S | I | P | A | F | A | V | T | G | D | T | D | Q | P | I | H | I | E | S | D | Q | Q | S | L | D | M | Q | G | N | V | V | T | F | T | G | N | V | I | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | T | Q | G | T | I | K | I | N | A | D | K | V | V | V | T | R | P | G | G | E | Q | G | K | E | V | I | D | G | Y | G | K | P | A | T | F | Y | Q | M | Q | D | N | G | K | P | V | E | G | H | A | S | Q | M | H | Y | E | L | A | K | D | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | V | V | L | T | G | N | A | Y | L | Q | Q | V | D | S | N | I | K | G | D | K | I | T | Y | L | V | K | E | Q | K | M | Q | A | F | S | D | K | G | K | R | V | T | T | V | L | V | P | S | Q | L | Q | D | K | N | N | K | G | Q | T | P | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | .
Sequence |  | Q | K | K | G | N
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 |
| c2r1aD_ |

### PDB 2r1a chain D

Region: 28 - 166
Aligned: 136
Modelled: 139
Confidence: 100.0%
Identity: 99%
PDB header:transport protein
Chain: D: PDB Molecule:protein yhbn;
PDBTitle: crystal structure of the periplasmic lipopolysaccharide transport2 protein lpta (yhbn), trigonal form

Phyre2
2 |
| c3my2A_ |

### PDB 3my2 chain A

Region: 37 - 165
Aligned: 118
Modelled: 129
Confidence: 98.8%
Identity: 19%
PDB header:transport protein
Chain: A: PDB Molecule:lipopolysaccharide export system protein lptc;
PDBTitle: crystal structure of lptc

Phyre2
3 |
| d1g7sa1 |

### PDB 1g7s chain A domain 1

Region: 145 - 174
Aligned: 30
Modelled: 30
Confidence: 25.0%
Identity: 17%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Translation proteins
Family: Elongation factors

Phyre2
4 |
| d1ueba3 |

### PDB 1ueb chain A domain 3

Region: 118 - 151
Aligned: 34
Modelled: 34
Confidence: 8.6%
Identity: 15%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2
5 |
| c1xctL_ |

### PDB 1xct chain L

Region: 29 - 56
Aligned: 28
Modelled: 28
Confidence: 7.2%
Identity: 14%
PDB header:immune system
Chain: L: PDB Molecule:protein l;
PDBTitle: complex hcv core-fab 19d9d6-protein l mutant (d55a, l57h, y64w) in2 space group p21212

Phyre2
6 |
| d2ptla_ |

### PDB 2ptl chain A

Region: 31 - 56
Aligned: 26
Modelled: 26
Confidence: 7.1%
Identity: 15%
Fold: beta-Grasp (ubiquitin-like)
Superfamily: Immunoglobulin-binding domains
Family: Immunoglobulin-binding domains

Phyre2
7 |
| c2jmbA_ |

### PDB 2jmb chain A

Region: 111 - 148
Aligned: 38
Modelled: 38
Confidence: 6.8%
Identity: 16%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein atu4866;
PDBTitle: solution structure of the protein atu4866 from agrobacterium2 tumefaciens

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2r1aD_ |
|  | 100.0 | 99 | PDB header:transport protein Chain: D: PDB Molecule:protein yhbn; PDBTitle: crystal structure of the periplasmic lipopolysaccharide transport2 protein lpta (yhbn), trigonal form
2 | c3my2A_ |
|  | 98.8 | 19 | PDB header:transport protein Chain: A: PDB Molecule:lipopolysaccharide export system protein lptc; PDBTitle: crystal structure of lptc
3 | d1g7sa1 |
|  | 25.0 | 17 | Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors
4 | d1ueba3 |
|  | 8.6 | 15 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
5 | c1xctL_ |
|  | 7.2 | 14 | PDB header:immune system Chain: L: PDB Molecule:protein l; PDBTitle: complex hcv core-fab 19d9d6-protein l mutant (d55a, l57h, y64w) in2 space group p21212
6 | d2ptla_ |
|  | 7.1 | 15 | Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains
7 | c2jmbA_ |
|  | 6.8 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein atu4866; PDBTitle: solution structure of the protein atu4866 from agrobacterium2 tumefaciens

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
Disclaimer
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