Phyre 2 Results for Q47152

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Email | l.a.kelley@imperial.ac.uk
Description | Q47152
Date | Thu Jan 5 12:36:27 GMT 2012
Unique Job ID | f9e8c21fa367e305

Summary |

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

Model (left) based on template d2f5ga1
Top template information
Fold:Ferredoxin-like Superfamily:Transposase IS200-like Family:Transposase IS200-like
Confidence and coverage
Confidence: | 99.9% | Coverage: | 73%
120 residues ( 73% 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 | E | Y | R | R | Y | Y | I | K | G | G | T | W | F | F | T | V | N | L | R | N | R | R | S | Q | L | L | T | T | Q | Y | Q | M | L | R | H | A | I | I | K | V | K | R | D | R | P | F | E | I | N | A | W | V | V | L | P | E | H | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | H | C | I | W | T | L | P | E | G | D | D | D | F | S | S | R | W | R | E | I | K | K | Q | F | T | H | A | C | G | L | K | N | I | W | Q | P | R | F | W | E | H | A | I | R | N | T | K | D | Y | R | H | H | V | D | Y | I | Y | I | N | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | .
Sequence |  | V | K | H | G | W | V | K | Q | V | S | D | W | P | F | S | T | F | H | R | D | V | A | R | G | L | Y | P | I | D | W | A | G | D | V | T | D | F | S | A | G | E | R | I | I | S
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 |
| d2f5ga1 |

### PDB 2f5g chain A domain 1

Region: 3 - 124
Aligned: 120
Modelled: 122
Confidence: 99.9%
Identity: 18%
Fold: Ferredoxin-like
Superfamily: Transposase IS200-like
Family: Transposase IS200-like

Phyre2
2 |
| d2fyxa1 |

### PDB 2fyx chain A domain 1

Region: 3 - 118
Aligned: 114
Modelled: 116
Confidence: 99.9%
Identity: 15%
Fold: Ferredoxin-like
Superfamily: Transposase IS200-like
Family: Transposase IS200-like

Phyre2
3 |
| c2vhgB_ |

### PDB 2vhg chain B

Region: 1 - 118
Aligned: 116
Modelled: 118
Confidence: 99.9%
Identity: 14%
PDB header:dna-binding protein
Chain: B: PDB Molecule:transposase orfa;
PDBTitle: crystal structure of the ishp608 transposase in complex2 with right end 31-mer dna

Phyre2
4 |
| d2vjva1 |

### PDB 2vjv chain A domain 1

Region: 1 - 118
Aligned: 116
Modelled: 118
Confidence: 99.9%
Identity: 14%
Fold: Ferredoxin-like
Superfamily: Transposase IS200-like
Family: Transposase IS200-like

Phyre2
5 |
| d1nzya_ |

### PDB 1nzy chain A

Region: 1 - 60
Aligned: 60
Modelled: 60
Confidence: 19.2%
Identity: 17%
Fold: ClpP/crotonase
Superfamily: ClpP/crotonase
Family: Crotonase-like

Phyre2
6 |
| c2ej5B_ |

### PDB 2ej5 chain B

Region: 1 - 60
Aligned: 60
Modelled: 60
Confidence: 18.3%
Identity: 17%
PDB header:lyase
Chain: B: PDB Molecule:enoyl-coa hydratase subunit ii;
PDBTitle: crystal structure of gk2038 protein (enoyl-coa hydratase subunit ii)2 from geobacillus kaustophilus

Phyre2
7 |
| d1qgva_ |

### PDB 1qgv chain A

Region: 103 - 132
Aligned: 30
Modelled: 30
Confidence: 17.3%
Identity: 17%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: spliceosomal protein U5-15Kd

Phyre2
8 |
| c2hldH_ |

### PDB 2hld chain H

Region: 52 - 69
Aligned: 18
Modelled: 18
Confidence: 15.6%
Identity: 28%
PDB header:hydrolase
Chain: H: PDB Molecule:atp synthase delta chain, mitochondrial;
PDBTitle: crystal structure of yeast mitochondrial f1-atpase

Phyre2
9 |
| c2vx2D_ |

### PDB 2vx2 chain D

Region: 2 - 60
Aligned: 59
Modelled: 59
Confidence: 13.7%
Identity: 8%
PDB header:isomerase
Chain: D: PDB Molecule:enoyl-coa hydratase domain-containing protein 3;
PDBTitle: crystal structure of human enoyl coenzyme a hydratase2 domain-containing protein 3 (echdc3)

Phyre2
10 |
| d2al3a1 |

### PDB 2al3 chain A domain 1

Region: 16 - 56
Aligned: 41
Modelled: 41
Confidence: 13.4%
Identity: 15%
Fold: beta-Grasp (ubiquitin-like)
Superfamily: Ubiquitin-like
Family: UBX domain

Phyre2
11 |
| c2rq7A_ |

### PDB 2rq7 chain A

Region: 53 - 69
Aligned: 17
Modelled: 17
Confidence: 12.9%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:atp synthase epsilon chain;
PDBTitle: solution structure of the epsilon subunit chimera combining2 the n-terminal beta-sandwich domain from t. elongatus bp-13 f1 and the c-terminal alpha-helical domain from spinach4 chloroplast f1

Phyre2
12 |
| c1fs0E_ |

### PDB 1fs0 chain E

Region: 52 - 69
Aligned: 18
Modelled: 18
Confidence: 11.8%
Identity: 17%
PDB header:hydrolase
Chain: E: PDB Molecule:atp synthase epsilon subunit;
PDBTitle: complex of gamma/epsilon atp synthase from e.coli

Phyre2
13 |
| d1y0ua_ |

### PDB 1y0u chain A

Region: 107 - 131
Aligned: 25
Modelled: 25
Confidence: 11.5%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: ArsR-like transcriptional regulators

Phyre2
14 |
| d3euga_ |

### PDB 3eug chain A

Region: 134 - 158
Aligned: 25
Modelled: 25
Confidence: 9.7%
Identity: 28%
Fold: Uracil-DNA glycosylase-like
Superfamily: Uracil-DNA glycosylase-like
Family: Uracil-DNA glycosylase

Phyre2
15 |
| c3i0uA_ |

### PDB 3i0u chain A

Region: 109 - 138
Aligned: 30
Modelled: 30
Confidence: 9.5%
Identity: 13%
PDB header:lyase
Chain: A: PDB Molecule:phosphothreonine lyase ospf;
PDBTitle: structure of the type iii effector/phosphothreonine lyase ospf from2 shigella flexneri

Phyre2
16 |
| c2x3gA_ |

### PDB 2x3g chain A

Region: 12 - 76
Aligned: 63
Modelled: 65
Confidence: 9.4%
Identity: 14%
PDB header:viral protein
Chain: A: PDB Molecule:sirv1 hypothetical protein orf119;
PDBTitle: crystal structure of the hypothetical protein orf119 from2 sulfolobus islandicus rod-shaped virus 1

Phyre2
17 |
| d1nvma1 |

### PDB 1nvm chain A domain 1

Region: 134 - 149
Aligned: 16
Modelled: 16
Confidence: 9.0%
Identity: 31%
Fold: RuvA C-terminal domain-like
Superfamily: post-HMGL domain-like
Family: DmpG/LeuA communication domain-like

Phyre2
18 |
| c3tr7A_ |

### PDB 3tr7 chain A

Region: 134 - 151
Aligned: 18
Modelled: 18
Confidence: 8.9%
Identity: 39%
PDB header:hydrolase
Chain: A: PDB Molecule:uracil-dna glycosylase;
PDBTitle: structure of a uracil-dna glycosylase (ung) from coxiella burnetii

Phyre2
19 |
| c3trrA_ |

### PDB 3trr chain A

Region: 1 - 60
Aligned: 60
Modelled: 60
Confidence: 7.9%
Identity: 12%
PDB header:isomerase
Chain: A: PDB Molecule:probable enoyl-coa hydratase/isomerase;
PDBTitle: crystal structure of a probable enoyl-coa hydratase/isomerase from2 mycobacterium abscessus

Phyre2
20 |
| d1aqta2 |

### PDB 1aqt chain A domain 2

Region: 52 - 69
Aligned: 18
Modelled: 18
Confidence: 7.6%
Identity: 17%
Fold: Epsilon subunit of F1F0-ATP synthase N-terminal domain
Superfamily: Epsilon subunit of F1F0-ATP synthase N-terminal domain
Family: Epsilon subunit of F1F0-ATP synthase N-terminal domain

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2f5ga1 |
|  | 99.9 | 18 | Fold:Ferredoxin-like Superfamily:Transposase IS200-like Family:Transposase IS200-like
2 | d2fyxa1 |
|  | 99.9 | 15 | Fold:Ferredoxin-like Superfamily:Transposase IS200-like Family:Transposase IS200-like
3 | c2vhgB_ |
|  | 99.9 | 14 | PDB header:dna-binding protein Chain: B: PDB Molecule:transposase orfa; PDBTitle: crystal structure of the ishp608 transposase in complex2 with right end 31-mer dna
4 | d2vjva1 |
|  | 99.9 | 14 | Fold:Ferredoxin-like Superfamily:Transposase IS200-like Family:Transposase IS200-like
5 | d1nzya_ |
|  | 19.2 | 17 | Fold:ClpP/crotonase Superfamily:ClpP/crotonase Family:Crotonase-like
6 | c2ej5B_ |
|  | 18.3 | 17 | PDB header:lyase Chain: B: PDB Molecule:enoyl-coa hydratase subunit ii; PDBTitle: crystal structure of gk2038 protein (enoyl-coa hydratase subunit ii)2 from geobacillus kaustophilus
7 | d1qgva_ |
|  | 17.3 | 17 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:spliceosomal protein U5-15Kd
8 | c2hldH_ |
|  | 15.6 | 28 | PDB header:hydrolase Chain: H: PDB Molecule:atp synthase delta chain, mitochondrial; PDBTitle: crystal structure of yeast mitochondrial f1-atpase
9 | c2vx2D_ |
|  | 13.7 | 8 | PDB header:isomerase Chain: D: PDB Molecule:enoyl-coa hydratase domain-containing protein 3; PDBTitle: crystal structure of human enoyl coenzyme a hydratase2 domain-containing protein 3 (echdc3)
10 | d2al3a1 |
|  | 13.4 | 15 | Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:UBX domain
11 | c2rq7A_ |
|  | 12.9 | 24 | PDB header:hydrolase Chain: A: PDB Molecule:atp synthase epsilon chain; PDBTitle: solution structure of the epsilon subunit chimera combining2 the n-terminal beta-sandwich domain from t. elongatus bp-13 f1 and the c-terminal alpha-helical domain from spinach4 chloroplast f1
12 | c1fs0E_ |
|  | 11.8 | 17 | PDB header:hydrolase Chain: E: PDB Molecule:atp synthase epsilon subunit; PDBTitle: complex of gamma/epsilon atp synthase from e.coli
13 | d1y0ua_ |
|  | 11.5 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
14 | d3euga_ |
|  | 9.7 | 28 | Fold:Uracil-DNA glycosylase-like Superfamily:Uracil-DNA glycosylase-like Family:Uracil-DNA glycosylase
15 | c3i0uA_ |
|  | 9.5 | 13 | PDB header:lyase Chain: A: PDB Molecule:phosphothreonine lyase ospf; PDBTitle: structure of the type iii effector/phosphothreonine lyase ospf from2 shigella flexneri
16 | c2x3gA_ |
|  | 9.4 | 14 | PDB header:viral protein Chain: A: PDB Molecule:sirv1 hypothetical protein orf119; PDBTitle: crystal structure of the hypothetical protein orf119 from2 sulfolobus islandicus rod-shaped virus 1
17 | d1nvma1 |
|  | 9.0 | 31 | Fold:RuvA C-terminal domain-like Superfamily:post-HMGL domain-like Family:DmpG/LeuA communication domain-like
18 | c3tr7A_ |
|  | 8.9 | 39 | PDB header:hydrolase Chain: A: PDB Molecule:uracil-dna glycosylase; PDBTitle: structure of a uracil-dna glycosylase (ung) from coxiella burnetii
19 | c3trrA_ |
|  | 7.9 | 12 | PDB header:isomerase Chain: A: PDB Molecule:probable enoyl-coa hydratase/isomerase; PDBTitle: crystal structure of a probable enoyl-coa hydratase/isomerase from2 mycobacterium abscessus
20 | d1aqta2 |
|  | 7.6 | 17 | Fold:Epsilon subunit of F1F0-ATP synthase N-terminal domain Superfamily:Epsilon subunit of F1F0-ATP synthase N-terminal domain Family:Epsilon subunit of F1F0-ATP synthase N-terminal domain
21 | d1laue_ |
| not modelled | 7.4 | 37 | Fold:Uracil-DNA glycosylase-like Superfamily:Uracil-DNA glycosylase-like Family:Uracil-DNA glycosylase
22 | c2qe7H_ |
| not modelled | 7.2 | 17 | PDB header:hydrolase Chain: H: PDB Molecule:atp synthase subunit epsilon; PDBTitle: crystal structure of the f1-atpase from the thermoalkaliphilic2 bacterium bacillus sp. ta2.a1
23 | c2owrD_ |
| not modelled | 6.9 | 20 | PDB header:hydrolase Chain: D: PDB Molecule:uracil-dna glycosylase; PDBTitle: crystal structure of vaccinia virus uracil-dna glycosylase
24 | c2e5yA_ |
| not modelled | 6.5 | 22 | PDB header:hydrolase Chain: A: PDB Molecule:atp synthase epsilon chain; PDBTitle: epsilon subunit and atp complex of f1f0-atp synthase from2 the thermophilic bacillus ps3
25 | c3swxB_ |
| not modelled | 6.2 | 15 | PDB header:isomerase Chain: B: PDB Molecule:probable enoyl-coa hydratase/isomerase; PDBTitle: crystal structure of a probable enoyl-coa hydratase/isomerase from2 mycobacterium abscessus
26 | d2hxma1 |
| not modelled | 6.0 | 37 | Fold:Uracil-DNA glycosylase-like Superfamily:Uracil-DNA glycosylase-like Family:Uracil-DNA glycosylase
27 | d1ysja1 |
| not modelled | 5.7 | 7 | Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases
28 | c1h8eH_ |
| not modelled | 5.6 | 28 | PDB header:hydrolase Chain: H: PDB Molecule:bovine mitochondrial f1-atpase; PDBTitle: (adp.alf4)2(adp.so4) bovine f1-atpase2 (all three catalytic sites occupied)
29 | d2aqaa1 |
| not modelled | 5.2 | 32 | Fold:Rubredoxin-like Superfamily:Nop10-like SnoRNP Family:Nucleolar RNA-binding protein Nop10-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