Phyre 2 Results for P10905

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Email | l.a.kelley@imperial.ac.uk
Description | P10905
Date | Wed Jan 25 15:20:37 GMT 2012
Unique Job ID | 08543d9e34881e8a

Summary |

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

Model (left) based on template c3fh6F_
Top template information
PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli
Confidence and coverage
Confidence: | 100.0% | Coverage: | 98%
288 residues ( 98% 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 | S | S | S | R | P | V | F | R | S | R | W | L | P | Y | L | L | V | A | P | Q | L | I | I | T | V | I | F | F | I | W | P | A | G | E | A | L | W | Y | S | L | Q | S | V | D | P | F | G | F | S | S | Q | F | V | G | L | D | N | F | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | T | L | F | H | D | S | Y | Y | L | D | S | F | W | T | T | I | K | F | S | T | F | V | T | V | S | G | L | L | V | S | L | F | F | A | A | L | V | E | Y | I | V | R | G | S | R | F | Y | Q | T | L | M | L | L | P | Y | A | V | A | P | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | V | A | A | V | L | W | I | F | L | F | N | P | G | R | G | L | I | T | H | F | L | A | E | F | G | Y | D | W | N | H | A | Q | N | S | G | Q | A | M | F | L | V | V | F | A | S | V | W | K | Q | I | S | Y | N | F | L | F | F | Y | A | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | L | Q | S | I | P | R | S | L | I | E | A | A | A | I | D | G | A | G | P | I | R | R | F | F | K | I | A | L | P | L | I | A | P | V | S | F | F | L | L | V | V | N | L | V | Y | A | F | F | D | T | F | P | V | I | D | A | A | T | S | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | .
Sequence |  | G | P | V | Q | A | T | T | T | L | I | Y | K | I | Y | R | E | G | F | T | G | L | D | L | A | S | S | A | A | Q | S | V | V | L | M | F | L | V | I | V | L | T | V | V | Q | F | R | Y | V | E | S | K | V | R | 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 |
| c3fh6F_ |

### PDB 3fh6 chain F

Region: 6 - 293
Aligned: 288
Modelled: 288
Confidence: 100.0%
Identity: 24%
PDB header:transport protein
Chain: F: PDB Molecule:maltose transport system permease protein malf;
PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli

Phyre2
2 |
| c2r6gF_ |

### PDB 2r6g chain F

Region: 51 - 283
Aligned: 233
Modelled: 233
Confidence: 100.0%
Identity: 30%
PDB header:hydrolase/transport protein
Chain: F: PDB Molecule:maltose transport system permease protein malf;
PDBTitle: the crystal structure of the e. coli maltose transporter

Phyre2
3 |
| d2r6gg1 |

### PDB 2r6g chain G domain 1

Region: 9 - 293
Aligned: 268
Modelled: 271
Confidence: 100.0%
Identity: 17%
Fold: MetI-like
Superfamily: MetI-like
Family: MetI-like

Phyre2
4 |
| d2r6gf2 |

### PDB 2r6g chain F domain 2

Region: 56 - 283
Aligned: 228
Modelled: 228
Confidence: 100.0%
Identity: 30%
Fold: MetI-like
Superfamily: MetI-like
Family: MetI-like

Phyre2
5 |
| d2onkc1 |

### PDB 2onk chain C domain 1

Region: 11 - 288
Aligned: 249
Modelled: 268
Confidence: 100.0%
Identity: 19%
Fold: MetI-like
Superfamily: MetI-like
Family: MetI-like

Phyre2
6 |
| c2onkC_ |

### PDB 2onk chain C

Region: 11 - 288
Aligned: 249
Modelled: 268
Confidence: 100.0%
Identity: 19%
PDB header:membrane protein
Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease
PDBTitle: abc transporter modbc in complex with its binding protein2 moda

Phyre2
7 |
| d3d31c1 |

### PDB 3d31 chain C domain 1

Region: 16 - 285
Aligned: 244
Modelled: 262
Confidence: 100.0%
Identity: 18%
Fold: MetI-like
Superfamily: MetI-like
Family: MetI-like

Phyre2
8 |
| c3d31D_ |

### PDB 3d31 chain D

Region: 16 - 285
Aligned: 244
Modelled: 262
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease
PDBTitle: modbc from methanosarcina acetivorans

Phyre2
9 |
| d3dhwa1 |

### PDB 3dhw chain A domain 1

Region: 68 - 283
Aligned: 197
Modelled: 216
Confidence: 99.9%
Identity: 18%
Fold: MetI-like
Superfamily: MetI-like
Family: MetI-like

Phyre2
10 |
| d2r6gf1 |

### PDB 2r6g chain F domain 1

Region: 7 - 51
Aligned: 45
Modelled: 45
Confidence: 95.5%
Identity: 9%
Fold: MalF N-terminal region-like
Superfamily: MalF N-terminal region-like
Family: MalF N-terminal region-like

Phyre2
11 |
| c1umqA_ |

### PDB 1umq chain A

Region: 176 - 206
Aligned: 31
Modelled: 31
Confidence: 46.5%
Identity: 10%
PDB header:dna-binding protein
Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein;
PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity

Phyre2
12 |
| d1umqa_ |

### PDB 1umq chain A

Region: 176 - 206
Aligned: 31
Modelled: 31
Confidence: 46.5%
Identity: 10%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
13 |
| d1fipa_ |

### PDB 1fip chain A

Region: 176 - 206
Aligned: 31
Modelled: 31
Confidence: 40.9%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
14 |
| d1ntca_ |

### PDB 1ntc chain A

Region: 175 - 206
Aligned: 32
Modelled: 32
Confidence: 38.5%
Identity: 25%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
15 |
| d1etob_ |

### PDB 1eto chain B

Region: 176 - 206
Aligned: 31
Modelled: 31
Confidence: 36.7%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
16 |
| d1etxa_ |

### PDB 1etx chain A

Region: 176 - 206
Aligned: 31
Modelled: 31
Confidence: 36.1%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
17 |
| c3e7lD_ |

### PDB 3e7l chain D

Region: 176 - 206
Aligned: 31
Modelled: 31
Confidence: 31.7%
Identity: 23%
PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain

Phyre2
18 |
| d1g2ha_ |

### PDB 1g2h chain A

Region: 176 - 206
Aligned: 30
Modelled: 31
Confidence: 24.0%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
19 |
| c2hx6A_ |

### PDB 2hx6 chain A

Region: 175 - 200
Aligned: 26
Modelled: 26
Confidence: 12.9%
Identity: 19%
PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease;
PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb

Phyre2
20 |
| c2cw1A_ |

### PDB 2cw1 chain A

Region: 185 - 199
Aligned: 15
Modelled: 15
Confidence: 7.1%
Identity: 20%
PDB header:de novo protein
Chain: A: PDB Molecule:sn4m;
PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein

Phyre2
21 |
22 |
23 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3fh6F_ |
|  | 100.0 | 24 | PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli
2 | c2r6gF_ |
|  | 100.0 | 30 | PDB header:hydrolase/transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: the crystal structure of the e. coli maltose transporter
3 | d2r6gg1 |
|  | 100.0 | 17 | Fold:MetI-like Superfamily:MetI-like Family:MetI-like
4 | d2r6gf2 |
|  | 100.0 | 30 | Fold:MetI-like Superfamily:MetI-like Family:MetI-like
5 | d2onkc1 |
|  | 100.0 | 19 | Fold:MetI-like Superfamily:MetI-like Family:MetI-like
6 | c2onkC_ |
|  | 100.0 | 19 | PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda
7 | d3d31c1 |
|  | 100.0 | 18 | Fold:MetI-like Superfamily:MetI-like Family:MetI-like
8 | c3d31D_ |
|  | 100.0 | 18 | PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans
9 | d3dhwa1 |
|  | 99.9 | 18 | Fold:MetI-like Superfamily:MetI-like Family:MetI-like
10 | d2r6gf1 |
|  | 95.5 | 9 | Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like
11 | c1umqA_ |
|  | 46.5 | 10 | PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
12 | d1umqa_ |
|  | 46.5 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
13 | d1fipa_ |
|  | 40.9 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
14 | d1ntca_ |
|  | 38.5 | 25 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
15 | d1etob_ |
|  | 36.7 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
16 | d1etxa_ |
|  | 36.1 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
17 | c3e7lD_ |
|  | 31.7 | 23 | PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
18 | d1g2ha_ |
|  | 24.0 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like
19 | c2hx6A_ |
|  | 12.9 | 19 | PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb
20 | c2cw1A_ |
|  | 7.1 | 20 | PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein
21 | d1v54g_ |
| not modelled | 5.3 | 21 | Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIa Family:Mitochondrial cytochrome c oxidase subunit VIa
22 | c1twcF_ |
| not modelled | 5.2 | 29 | PDB header:transcription Chain: F: PDB Molecule:dna-directed rna polymerases i, ii, and iii 23 PDBTitle: rna polymerase ii complexed with gtp
23 | d1twff_ |
| not modelled | 5.2 | 29 | Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RPB6

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