Phyre 2 Results for Q1PI54

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Email | l.a.kelley@imperial.ac.uk
Description | Q1PI54
Date | Thu Jan 5 12:33:28 GMT 2012
Unique Job ID | 7e0b62bdb8f5f2e7

Summary |

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

Model (left) based on template d3b8ma1
Top template information
Fold:Ferredoxin-like Superfamily:Bacterial polysaccharide co-polymerase-like Family:FepE-like
Confidence and coverage
Confidence: | 100.0% | Coverage: | 89%
128 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 |  | L | L | I | S | F | I | L | P | Q | K | W | T | S | A | A | V | V | T | P | P | E | P | V | Q | W | Q | E | L | E | K | S | F | T | K | L | R | V | L | D | L | D | I | K | I | D | R | T | E | A | F | N | L | F | I | K | K | F | Q | S | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  | ? | ? |  |  |  |  |  | ? |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | S | L | L | E | E | Y | L | R | S | S | P | Y | V | M | D | Q | L | K | E | A | K | I | D | E | L | D | L | H | R | A | I | V | A | L | S | E | K | M | K | A | V | D | D | N | A | S | K | K | K | D | E | P | S | L | Y | T | S | W | T | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | .
Sequence |  | S | F | T | A | P | T | S | E | E | A | Q | T | V | L | S | G | Y | I | D | Y | I | S | T | L
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 |
| d3b8ma1 |

### PDB 3b8m chain A domain 1

Region: 10 - 143
Aligned: 128
Modelled: 134
Confidence: 100.0%
Identity: 98%
Fold: Ferredoxin-like
Superfamily: Bacterial polysaccharide co-polymerase-like
Family: FepE-like

Phyre2
2 |
| d3b8oa1 |

### PDB 3b8o chain A domain 1

Region: 10 - 143
Aligned: 122
Modelled: 128
Confidence: 100.0%
Identity: 16%
Fold: Ferredoxin-like
Superfamily: Bacterial polysaccharide co-polymerase-like
Family: FepE-like

Phyre2
3 |
| d3b8pa1 |

### PDB 3b8p chain A domain 1

Region: 9 - 143
Aligned: 104
Modelled: 104
Confidence: 99.9%
Identity: 24%
Fold: Ferredoxin-like
Superfamily: Bacterial polysaccharide co-polymerase-like
Family: FepE-like

Phyre2
4 |
| d1p5dx4 |

### PDB 1p5d chain X domain 4

Region: 118 - 144
Aligned: 27
Modelled: 27
Confidence: 21.2%
Identity: 22%
Fold: TBP-like
Superfamily: Phosphoglucomutase, C-terminal domain
Family: Phosphoglucomutase, C-terminal domain

Phyre2
5 |
| d1mixa2 |

### PDB 1mix chain A domain 2

Region: 119 - 141
Aligned: 23
Modelled: 23
Confidence: 17.2%
Identity: 30%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Third domain of FERM

Phyre2
6 |
| d1mjia_ |

### PDB 1mji chain A

Region: 117 - 137
Aligned: 21
Modelled: 21
Confidence: 11.2%
Identity: 33%
Fold: RL5-like
Superfamily: RL5-like
Family: Ribosomal protein L5

Phyre2
7 |
| c3bboH_ |

### PDB 3bbo chain H

Region: 117 - 137
Aligned: 21
Modelled: 21
Confidence: 10.0%
Identity: 33%
PDB header:ribosome
Chain: H: PDB Molecule:ribosomal protein l5;
PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome

Phyre2
8 |
| d2zjrd1 |

### PDB 2zjr chain D domain 1

Region: 117 - 137
Aligned: 21
Modelled: 21
Confidence: 10.0%
Identity: 38%
Fold: RL5-like
Superfamily: RL5-like
Family: Ribosomal protein L5

Phyre2
9 |
| c1mk7B_ |

### PDB 1mk7 chain B

Region: 119 - 141
Aligned: 23
Modelled: 23
Confidence: 9.9%
Identity: 30%
PDB header:structural protein
Chain: B: PDB Molecule:talin;
PDBTitle: crystal structure of an integrin beta3-talin chimera

Phyre2
10 |
| d1iq4a_ |

### PDB 1iq4 chain A

Region: 117 - 137
Aligned: 21
Modelled: 21
Confidence: 8.2%
Identity: 33%
Fold: RL5-like
Superfamily: RL5-like
Family: Ribosomal protein L5

Phyre2
11 |
| c2k9iB_ |

### PDB 2k9i chain B

Region: 3 - 11
Aligned: 9
Modelled: 9
Confidence: 7.7%
Identity: 33%
PDB header:dna binding protein
Chain: B: PDB Molecule:plasmid prn1, complete sequence;
PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus

Phyre2
12 |
| c2jvfA_ |

### PDB 2jvf chain A

Region: 82 - 139
Aligned: 46
Modelled: 58
Confidence: 7.6%
Identity: 17%
PDB header:de novo protein
Chain: A: PDB Molecule:de novo protein m7;
PDBTitle: solution structure of m7, a computationally-designed2 artificial protein

Phyre2
13 |
| c3g9wA_ |

### PDB 3g9w chain A

Region: 119 - 141
Aligned: 23
Modelled: 23
Confidence: 7.2%
Identity: 30%
PDB header:cell adhesion
Chain: A: PDB Molecule:talin-2;
PDBTitle: crystal structure of talin2 f2-f3 in complex with the integrin beta1d2 cytoplasmic tail

Phyre2
14 |
| d1eika_ |

### PDB 1eik chain A

Region: 126 - 137
Aligned: 12
Modelled: 12
Confidence: 7.1%
Identity: 33%
Fold: RPB5-like RNA polymerase subunit
Superfamily: RPB5-like RNA polymerase subunit
Family: RPB5

Phyre2
15 |
| d1dzfa2 |

### PDB 1dzf chain A domain 2

Region: 126 - 137
Aligned: 12
Modelled: 12
Confidence: 6.9%
Identity: 33%
Fold: RPB5-like RNA polymerase subunit
Superfamily: RPB5-like RNA polymerase subunit
Family: RPB5

Phyre2
16 |
| c2pmzV_ |

### PDB 2pmz chain V

Region: 126 - 137
Aligned: 12
Modelled: 12
Confidence: 6.9%
Identity: 25%
PDB header:translation, transferase
Chain: V: PDB Molecule:dna-directed rna polymerase subunit h;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus

Phyre2
17 |
| d1hmja_ |

### PDB 1hmj chain A

Region: 126 - 137
Aligned: 12
Modelled: 12
Confidence: 6.3%
Identity: 33%
Fold: RPB5-like RNA polymerase subunit
Superfamily: RPB5-like RNA polymerase subunit
Family: RPB5

Phyre2
18 |
| d2a5yb2 |

### PDB 2a5y chain B domain 2

Region: 132 - 141
Aligned: 10
Modelled: 10
Confidence: 6.2%
Identity: 40%
Fold: DEATH domain
Superfamily: DEATH domain
Family: Caspase recruitment domain, CARD

Phyre2
19 |
| c3n7nE_ |

### PDB 3n7n chain E

Region: 41 - 55
Aligned: 15
Modelled: 15
Confidence: 6.1%
Identity: 20%
PDB header:replication
Chain: E: PDB Molecule:monopolin complex subunit lrs4;
PDBTitle: structure of csm1/lrs4 complex

Phyre2
20 |
| d1uuja_ |

### PDB 1uuj chain A

Region: 6 - 13
Aligned: 8
Modelled: 8
Confidence: 6.0%
Identity: 63%
Fold: Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain
Superfamily: Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain
Family: Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain

Phyre2
21 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d3b8ma1 |
|  | 100.0 | 98 | Fold:Ferredoxin-like Superfamily:Bacterial polysaccharide co-polymerase-like Family:FepE-like
2 | d3b8oa1 |
|  | 100.0 | 16 | Fold:Ferredoxin-like Superfamily:Bacterial polysaccharide co-polymerase-like Family:FepE-like
3 | d3b8pa1 |
|  | 99.9 | 24 | Fold:Ferredoxin-like Superfamily:Bacterial polysaccharide co-polymerase-like Family:FepE-like
4 | d1p5dx4 |
|  | 21.2 | 22 | Fold:TBP-like Superfamily:Phosphoglucomutase, C-terminal domain Family:Phosphoglucomutase, C-terminal domain
5 | d1mixa2 |
|  | 17.2 | 30 | Fold:PH domain-like barrel Superfamily:PH domain-like Family:Third domain of FERM
6 | d1mjia_ |
|  | 11.2 | 33 | Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5
7 | c3bboH_ |
|  | 10.0 | 33 | PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein l5; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome
8 | d2zjrd1 |
|  | 10.0 | 38 | Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5
9 | c1mk7B_ |
|  | 9.9 | 30 | PDB header:structural protein Chain: B: PDB Molecule:talin; PDBTitle: crystal structure of an integrin beta3-talin chimera
10 | d1iq4a_ |
|  | 8.2 | 33 | Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5
11 | c2k9iB_ |
|  | 7.7 | 33 | PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus
12 | c2jvfA_ |
|  | 7.6 | 17 | PDB header:de novo protein Chain: A: PDB Molecule:de novo protein m7; PDBTitle: solution structure of m7, a computationally-designed2 artificial protein
13 | c3g9wA_ |
|  | 7.2 | 30 | PDB header:cell adhesion Chain: A: PDB Molecule:talin-2; PDBTitle: crystal structure of talin2 f2-f3 in complex with the integrin beta1d2 cytoplasmic tail
14 | d1eika_ |
|  | 7.1 | 33 | Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5
15 | d1dzfa2 |
|  | 6.9 | 33 | Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5
16 | c2pmzV_ |
|  | 6.9 | 25 | PDB header:translation, transferase Chain: V: PDB Molecule:dna-directed rna polymerase subunit h; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
17 | d1hmja_ |
|  | 6.3 | 33 | Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5
18 | d2a5yb2 |
|  | 6.2 | 40 | Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD
19 | c3n7nE_ |
|  | 6.1 | 20 | PDB header:replication Chain: E: PDB Molecule:monopolin complex subunit lrs4; PDBTitle: structure of csm1/lrs4 complex
20 | d1uuja_ |
|  | 6.0 | 63 | Fold:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Superfamily:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Family:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain
21 | d2j6ba1 |
| not modelled | 5.5 | 15 | Fold:STIV B116-like Superfamily:STIV B116-like Family:STIV B116-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