Phyre 2 Results for P39834

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Email | l.a.kelley@imperial.ac.uk
Description | P39834
Date | Thu Jan 5 12:01:00 GMT 2012
Unique Job ID | 4e60e0e3a09aced8

Summary |

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

Model (left) based on template c3jwnK_
Top template information
PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
Confidence and coverage
Confidence: | 99.9% | Coverage: | 82%
150 residues ( 82% of your sequence) have been modelled with 99.9% 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 | S | A | F | K | K | S | L | L | V | A | G | V | A | M | I | L | S | N | N | V | F | A | D | E | G | H | G | I | V | K | F | K | G | E | V | I | S | A | P | C | S | I | K | P | G | D | E | D | L | T | V | N | L | G | E | V | A | D | T
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | V | L | K | S | D | Q | K | S | L | A | E | P | F | T | I | H | L | Q | D | C | M | L | S | Q | G | G | T | T | Y | S | K | A | K | V | T | F | T | T | A | N | T | M | T | G | Q | S | D | L | L | K | N | T | K | E | T | E | I | G | G | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | T | G | V | G | V | R | I | L | D | S | Q | S | G | E | V | T | L | G | T | P | V | V | I | T | F | N | N | T | N | S | Y | Q | E | L | N | F | K | A | R | M | E | S | P | S | K | D | A | T | P | G | N | V | Y | A | Q | A | D | Y | K | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  |  |  |  |  |  |  |  | ? |  |  | ? |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | .
Sequence |  | A | Y | E
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 |
| c3jwnK_ |

### PDB 3jwn chain K

Region: 26 - 183
Aligned: 150
Modelled: 158
Confidence: 99.9%
Identity: 26%
PDB header:protein binding/cell adhesion
Chain: K: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
2 |
| c3jwnL_ |

### PDB 3jwn chain L

Region: 26 - 183
Aligned: 150
Modelled: 158
Confidence: 99.9%
Identity: 26%
PDB header:protein binding/cell adhesion
Chain: L: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
3 |
| c2jtyA_ |

### PDB 2jty chain A

Region: 21 - 183
Aligned: 157
Modelled: 163
Confidence: 99.9%
Identity: 34%
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
4 |
| c3jwnE_ |

### PDB 3jwn chain E

Region: 26 - 183
Aligned: 150
Modelled: 158
Confidence: 99.9%
Identity: 25%
PDB header:protein binding/cell adhesion
Chain: E: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
5 |
| d2j2zb1 |

### PDB 2j2z chain B domain 1

Region: 29 - 183
Aligned: 147
Modelled: 155
Confidence: 99.9%
Identity: 22%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
6 |
| c3jwnF_ |

### PDB 3jwn chain F

Region: 26 - 183
Aligned: 150
Modelled: 158
Confidence: 99.9%
Identity: 26%
PDB header:protein binding/cell adhesion
Chain: F: PDB Molecule:protein fimf;
PDBTitle: complex of fimc, fimf, fimg and fimh

Phyre2
7 |
| c2jmrA_ |

### PDB 2jmr chain A

Region: 26 - 183
Aligned: 150
Modelled: 153
Confidence: 99.9%
Identity: 25%
PDB header:cell adhesion
Chain: A: PDB Molecule:fimf;
PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf

Phyre2
8 |
| d2uy6b1 |

### PDB 2uy6 chain B domain 1

Region: 29 - 183
Aligned: 147
Modelled: 155
Confidence: 99.9%
Identity: 21%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
9 |
| c3bfwA_ |

### PDB 3bfw chain A

Region: 38 - 182
Aligned: 130
Modelled: 137
Confidence: 99.9%
Identity: 21%
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 |
| d1pdkb_ |

### PDB 1pdk chain B

Region: 36 - 183
Aligned: 140
Modelled: 148
Confidence: 99.9%
Identity: 21%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
11 |
| c3bwuF_ |

### PDB 3bwu chain F

Region: 38 - 183
Aligned: 125
Modelled: 141
Confidence: 99.8%
Identity: 25%
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
12 |
| c1klfP_ |

### PDB 1klf chain P

Region: 29 - 183
Aligned: 133
Modelled: 145
Confidence: 99.8%
Identity: 20%
PDB header:chaperone/adhesin complex
Chain: P: PDB Molecule:fimh protein;
PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose

Phyre2
13 |
| d1ze3h1 |

### PDB 1ze3 chain H domain 1

Region: 39 - 183
Aligned: 121
Modelled: 145
Confidence: 99.8%
Identity: 20%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
14 |
| c2w07B_ |

### PDB 2w07 chain B

Region: 35 - 182
Aligned: 119
Modelled: 148
Confidence: 99.7%
Identity: 22%
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
15 |
| d1n12a_ |

### PDB 1n12 chain A

Region: 39 - 182
Aligned: 129
Modelled: 144
Confidence: 99.4%
Identity: 18%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: Bacterial adhesins
Family: Pilus subunits

Phyre2
16 |
| c1w3gA_ |

### PDB 1w3g chain A

Region: 134 - 183
Aligned: 50
Modelled: 50
Confidence: 27.7%
Identity: 14%
PDB header:toxin/lectin
Chain: A: PDB Molecule:hemolytic lectin from laetiporus sulphureus;
PDBTitle: hemolytic lectin from the mushroom laetiporus sulphureus2 complexed with two n-acetyllactosamine molecules.

Phyre2
17 |
| d2jnaa1 |

### PDB 2jna chain A domain 1

Region: 1 - 26
Aligned: 24
Modelled: 26
Confidence: 11.8%
Identity: 29%
Fold: Dodecin subunit-like
Superfamily: YdgH-like
Family: YdgH-like

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3jwnK_ |
|  | 99.9 | 26 | PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
2 | c3jwnL_ |
|  | 99.9 | 26 | PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
3 | c2jtyA_ |
|  | 99.9 | 34 | 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
4 | c3jwnE_ |
|  | 99.9 | 25 | PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
5 | d2j2zb1 |
|  | 99.9 | 22 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
6 | c3jwnF_ |
|  | 99.9 | 26 | PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh
7 | c2jmrA_ |
|  | 99.9 | 25 | PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf
8 | d2uy6b1 |
|  | 99.9 | 21 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
9 | c3bfwA_ |
|  | 99.9 | 21 | 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 | d1pdkb_ |
|  | 99.9 | 21 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
11 | c3bwuF_ |
|  | 99.8 | 25 | 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)
12 | c1klfP_ |
|  | 99.8 | 20 | PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose
13 | d1ze3h1 |
|  | 99.8 | 20 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
14 | c2w07B_ |
|  | 99.7 | 22 | 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
15 | d1n12a_ |
|  | 99.4 | 18 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits
16 | c1w3gA_ |
|  | 27.7 | 14 | PDB header:toxin/lectin Chain: A: PDB Molecule:hemolytic lectin from laetiporus sulphureus; PDBTitle: hemolytic lectin from the mushroom laetiporus sulphureus2 complexed with two n-acetyllactosamine molecules.
17 | d2jnaa1 |
|  | 11.8 | 29 | Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-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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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