Phyre 2 Results for P75715

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Email | l.a.kelley@imperial.ac.uk
Description | P75715
Date | Thu Jan 5 12:13:24 GMT 2012
Unique Job ID | c334039bb9a7cd3b

Summary |

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

Model (left) based on template c2w07B_
Top template information
PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf
Confidence and coverage
Confidence: | 99.9% | Coverage: | 37%
121 residues ( 37% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
291 residues ( 89%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | A | M | A | C | L | C | L | A | N | I | S | W | A | T | V | C | A | N | S | T | G | V | A | E | D | E | H | Y | D | L | S | N | I | F | N | S | T | N | N | Q | P | G | Q | I | V | V | L | P | E | K | S | G | W | V | G | V | S | A | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  | ? |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | C | P | P | G | T | L | V | N | Y | T | Y | R | S | Y | V | T | N | F | I | V | Q | E | T | I | D | N | Y | K | Y | M | Q | L | H | D | Y | L | L | G | A | M | S | L | V | D | S | V | M | D | I | Q | F | P | P | Q | N | Y | I | R | M | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | T | D | P | N | V | S | Q | N | L | P | F | G | V | M | D | S | R | L | I | F | R | L | K | V | I | R | P | F | I | N | M | V | E | I | P | R | Q | V | M | F | T | V | Y | V | T | S | T | P | Y | D | P | L | V | T | P | V | Y | T | I | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  | ? |  |  |  | ? |  |  |  |  | ? | ? |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  | ? |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | F | G | G | R | V | E | V | P | Q | N | C | E | L | N | A | G | Q | I | V | E | F | D | F | G | D | I | G | A | S | L | F | S | A | A | G | P | G | N | R | P | A | G | V | M | P | Q | T | K | S | I | A | V | K | C | T | N | V | A | A | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  | ? |  | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | A | Y | L | T | M | R | L | E | A | S | A | V | S | G | Q | A | M | V | S | D | N | Q | D | L | G | F | I | V | A | D | Q | N | D | T | P | I | T | P | N | D | L | N | S | V | I | P | F | R | L | D | A | A | A | A | A | N | V | T | L | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  | ? |  | ? | ? |  |  |  |  |  |  |  | ? | ? | ? |  |  |  | ? | ? |  | ? | ? | ? | ? | ? |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | .
Sequence |  | A | W | P | I | S | I | T | G | Q | K | P | T | E | G | P | F | S | A | L | G | Y | L | R | V | D | Y | Q
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 |
| c2w07B_ |

### PDB 2w07 chain B

Region: 184 - 327
Aligned: 121
Modelled: 144
Confidence: 99.9%
Identity: 19%
PDB header:cell adhesion
Chain: B: PDB Molecule:minor pilin subunit papf;
PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf

Phyre2
2 |
| c1klfP_ |

### PDB 1klf chain P

Region: 16 - 327
Aligned: 268
Modelled: 292
Confidence: 99.9%
Identity: 17%
PDB header:chaperone/adhesin complex
Chain: P: PDB Molecule:fimh protein;
PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose

Phyre2
3 |
| d1n12a_ |

### PDB 1n12 chain A

Region: 189 - 326
Aligned: 128
Modelled: 138
Confidence: 99.9%
Identity: 17%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
4 |
| c3jwnL_ |

### PDB 3jwn chain L

Region: 178 - 327
Aligned: 144
Modelled: 150
Confidence: 99.9%
Identity: 17%
PDB header:protein binding/cell adhesion
Chain: L: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
5 |
| c3jwnK_ |

### PDB 3jwn chain K

Region: 178 - 327
Aligned: 144
Modelled: 150
Confidence: 99.9%
Identity: 17%
PDB header:protein binding/cell adhesion
Chain: K: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
6 |
| d2j2zb1 |

### PDB 2j2z chain B domain 1

Region: 178 - 327
Aligned: 144
Modelled: 150
Confidence: 99.8%
Identity: 16%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
7 |
| c3jwnF_ |

### PDB 3jwn chain F

Region: 178 - 327
Aligned: 144
Modelled: 150
Confidence: 99.8%
Identity: 17%
PDB header:protein binding/cell adhesion
Chain: F: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
8 |
| c3jwnE_ |

### PDB 3jwn chain E

Region: 178 - 327
Aligned: 144
Modelled: 150
Confidence: 99.8%
Identity: 17%
PDB header:protein binding/cell adhesion
Chain: E: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
9 |
| c3bfwA_ |

### PDB 3bfw chain A

Region: 188 - 326
Aligned: 131
Modelled: 139
Confidence: 99.8%
Identity: 14%
PDB header:structural protein/structural protein
Chain: A: PDB Molecule:protein fimg;
PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf)

Phyre2
10 |
| c2jmrA_ |

### PDB 2jmr chain A

Region: 178 - 327
Aligned: 144
Modelled: 150
Confidence: 99.8%
Identity: 18%
PDB header:cell adhesion
Chain: A: PDB Molecule:fimf;
PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf

Phyre2
11 |
| d2uy6b1 |

### PDB 2uy6 chain B domain 1

Region: 178 - 327
Aligned: 147
Modelled: 150
Confidence: 99.8%
Identity: 18%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
12 |
| d1pdkb_ |

### PDB 1pdk chain B

Region: 186 - 327
Aligned: 140
Modelled: 142
Confidence: 99.8%
Identity: 11%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
13 |
| c2jtyA_ |

### PDB 2jty chain A

Region: 179 - 327
Aligned: 142
Modelled: 149
Confidence: 99.8%
Identity: 20%
PDB header:structural protein
Chain: A: PDB Molecule:type-1 fimbrial protein, a chain;
PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus

Phyre2
14 |
| d1ze3h1 |

### PDB 1ze3 chain H domain 1

Region: 190 - 327
Aligned: 115
Modelled: 122
Confidence: 99.6%
Identity: 21%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
15 |
| c3bwuF_ |

### PDB 3bwu chain F

Region: 205 - 327
Aligned: 118
Modelled: 123
Confidence: 99.6%
Identity: 14%
PDB header:chaperone, structural, membrane protein
Chain: F: PDB Molecule:protein fimf;
PDBTitle: crystal structure of the ternary complex of fimd (n-terminal domain,2 fimdn) with fimc and the n-terminally truncated pilus subunit fimf3 (fimft)

Phyre2
16 |
| c2wmpB_ |

### PDB 2wmp chain B

Region: 191 - 326
Aligned: 118
Modelled: 136
Confidence: 84.1%
Identity: 18%
PDB header:chaperone
Chain: B: PDB Molecule:papg protein;
PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin

Phyre2
17 |
| d1p5vb_ |

### PDB 1p5v chain B

Region: 276 - 327
Aligned: 50
Modelled: 52
Confidence: 8.1%
Identity: 20%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2w07B_ |
|  | 99.9 | 19 | PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf
2 | c1klfP_ |
|  | 99.9 | 17 | PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose
3 | d1n12a_ |
|  | 99.9 | 17 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
4 | c3jwnL_ |
|  | 99.9 | 17 | PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
5 | c3jwnK_ |
|  | 99.9 | 17 | PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
6 | d2j2zb1 |
|  | 99.8 | 16 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
7 | c3jwnF_ |
|  | 99.8 | 17 | PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
8 | c3jwnE_ |
|  | 99.8 | 17 | PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
9 | c3bfwA_ |
|  | 99.8 | 14 | PDB header:structural protein/structural protein Chain: A: PDB Molecule:protein fimg; PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf)
10 | c2jmrA_ |
|  | 99.8 | 18 | PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf
11 | d2uy6b1 |
|  | 99.8 | 18 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
12 | d1pdkb_ |
|  | 99.8 | 11 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
13 | c2jtyA_ |
|  | 99.8 | 20 | PDB header:structural protein Chain: A: PDB Molecule:type-1 fimbrial protein, a chain; PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus
14 | d1ze3h1 |
|  | 99.6 | 21 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
15 | c3bwuF_ |
|  | 99.6 | 14 | PDB header:chaperone, structural, membrane protein Chain: F: PDB Molecule:protein fimf; PDBTitle: crystal structure of the ternary complex of fimd (n-terminal domain,2 fimdn) with fimc and the n-terminally truncated pilus subunit fimf3 (fimft)
16 | c2wmpB_ |
|  | 84.1 | 18 | PDB header:chaperone Chain: B: PDB Molecule:papg protein; PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin
17 | d1p5vb_ |
|  | 8.1 | 20 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits

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