Phyre 2 Results for Q46796

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Email | l.a.kelley@imperial.ac.uk
Description | Q46796
Date | Thu Jan 5 12:34:16 GMT 2012
Unique Job ID | 893a1a8d2189754b

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3hxxA_
Top template information
PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp
Confidence and coverage
Confidence: | 24.5% | Coverage: | 23%
23 residues ( 23% of your sequence) have been modelled with 24.5% confidence by the single highest scoring template.
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | T | S | G | L | E | R | L | S | N | L | L | S | K | K | D | S | V | F | V | S | D | L | L | R | E | A | K | V | N | E | L | D | E | T | L | S | T | T | R | L | N | H | L | I | D | K | G | Y | E | R | I | T | L | Q | L | D | L | G | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | .
Sequence |  | E | S | P | G | Y | L | E | K | D | K | H | Y | R | E | A | D | A | A | L | L | N | V | I | Y | P | T | N | L | S | K | I | N | T | R | R | K | E | Q | V
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 |
| c3hxxA_ |

### PDB 3hxx chain A

Region: 4 - 26
Aligned: 23
Modelled: 23
Confidence: 24.5%
Identity: 39%
PDB header:ligase
Chain: A: PDB Molecule:alanyl-trna synthetase;
PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp

Phyre2
2 |
| c2fb6A_ |

### PDB 2fb6 chain A

Region: 40 - 53
Aligned: 14
Modelled: 14
Confidence: 20.6%
Identity: 14%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: structure of conserved protein of unknown function bt1422 from2 bacteroides thetaiotaomicron

Phyre2
3 |
| c1yfsB_ |

### PDB 1yfs chain B

Region: 4 - 26
Aligned: 23
Modelled: 23
Confidence: 19.7%
Identity: 39%
PDB header:ligase
Chain: B: PDB Molecule:alanyl-trna synthetase;
PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine

Phyre2
4 |
| c2zzfA_ |

### PDB 2zzf chain A

Region: 4 - 23
Aligned: 20
Modelled: 20
Confidence: 12.1%
Identity: 30%
PDB header:ligase
Chain: A: PDB Molecule:alanyl-trna synthetase;
PDBTitle: crystal structure of alanyl-trna synthetase without2 oligomerization domain

Phyre2
5 |
| c3rf1B_ |

### PDB 3rf1 chain B

Region: 1 - 19
Aligned: 19
Modelled: 19
Confidence: 11.3%
Identity: 42%
PDB header:ligase
Chain: B: PDB Molecule:glycyl-trna synthetase alpha subunit;
PDBTitle: the crystal structure of glycyl-trna synthetase subunit alpha from2 campylobacter jejuni subsp. jejuni nctc 11168

Phyre2
6 |
| c2i3sF_ |

### PDB 2i3s chain F

Region: 80 - 93
Aligned: 14
Modelled: 14
Confidence: 10.1%
Identity: 50%
PDB header:cell cycle
Chain: F: PDB Molecule:checkpoint serine/threonine-protein kinase;
PDBTitle: bub3 complex with bub1 glebs motif

Phyre2
7 |
| d1j5wa_ |

### PDB 1j5w chain A

Region: 1 - 19
Aligned: 19
Modelled: 19
Confidence: 9.8%
Identity: 42%
Fold: Class II aaRS and biotin synthetases
Superfamily: Class II aaRS and biotin synthetases
Family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Phyre2
8 |
| d1ejxb_ |

### PDB 1ejx chain B

Region: 45 - 79
Aligned: 35
Modelled: 35
Confidence: 9.4%
Identity: 20%
Fold: beta-clip
Superfamily: Urease, beta-subunit
Family: Urease, beta-subunit

Phyre2
9 |
| d2psoa1 |

### PDB 2pso chain A domain 1

Region: 52 - 68
Aligned: 17
Modelled: 17
Confidence: 7.7%
Identity: 35%
Fold: TBP-like
Superfamily: Bet v1-like
Family: STAR domain

Phyre2
10 |
| d4ubpb_ |

### PDB 4ubp chain B

Region: 45 - 79
Aligned: 35
Modelled: 35
Confidence: 7.1%
Identity: 26%
Fold: beta-clip
Superfamily: Urease, beta-subunit
Family: Urease, beta-subunit

Phyre2
11 |
| d1e9ya1 |

### PDB 1e9y chain A domain 1

Region: 45 - 79
Aligned: 35
Modelled: 35
Confidence: 6.7%
Identity: 20%
Fold: beta-clip
Superfamily: Urease, beta-subunit
Family: Urease, beta-subunit

Phyre2
12 |
| c2k4bA_ |

### PDB 2k4b chain A

Region: 10 - 49
Aligned: 40
Modelled: 40
Confidence: 6.1%
Identity: 15%
PDB header:dna binding protein
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: copr repressor structure

Phyre2
13 |
| c2vn2B_ |

### PDB 2vn2 chain B

Region: 27 - 58
Aligned: 32
Modelled: 32
Confidence: 6.1%
Identity: 19%
PDB header:replication
Chain: B: PDB Molecule:chromosome replication initiation protein;
PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426

Phyre2
14 |
| c1avoA_ |

### PDB 1avo chain A

Region: 7 - 42
Aligned: 36
Modelled: 36
Confidence: 5.6%
Identity: 36%
PDB header:proteasome activator
Chain: A: PDB Molecule:11s regulator;
PDBTitle: proteasome activator reg(alpha)

Phyre2
15 |
| d1jb0k_ |

### PDB 1jb0 chain K

Region: 32 - 48
Aligned: 17
Modelled: 17
Confidence: 5.3%
Identity: 47%
Fold: Photosystem I reaction center subunit X, PsaK
Superfamily: Photosystem I reaction center subunit X, PsaK
Family: Photosystem I reaction center subunit X, PsaK

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3hxxA_ |
|  | 24.5 | 39 | PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp
2 | c2fb6A_ |
|  | 20.6 | 14 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: structure of conserved protein of unknown function bt1422 from2 bacteroides thetaiotaomicron
3 | c1yfsB_ |
|  | 19.7 | 39 | PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine
4 | c2zzfA_ |
|  | 12.1 | 30 | PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of alanyl-trna synthetase without2 oligomerization domain
5 | c3rf1B_ |
|  | 11.3 | 42 | PDB header:ligase Chain: B: PDB Molecule:glycyl-trna synthetase alpha subunit; PDBTitle: the crystal structure of glycyl-trna synthetase subunit alpha from2 campylobacter jejuni subsp. jejuni nctc 11168
6 | c2i3sF_ |
|  | 10.1 | 50 | PDB header:cell cycle Chain: F: PDB Molecule:checkpoint serine/threonine-protein kinase; PDBTitle: bub3 complex with bub1 glebs motif
7 | d1j5wa_ |
|  | 9.8 | 42 | Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
8 | d1ejxb_ |
|  | 9.4 | 20 | Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit
9 | d2psoa1 |
|  | 7.7 | 35 | Fold:TBP-like Superfamily:Bet v1-like Family:STAR domain
10 | d4ubpb_ |
|  | 7.1 | 26 | Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit
11 | d1e9ya1 |
|  | 6.7 | 20 | Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit
12 | c2k4bA_ |
|  | 6.1 | 15 | PDB header:dna binding protein Chain: A: PDB Molecule:transcriptional regulator; PDBTitle: copr repressor structure
13 | c2vn2B_ |
|  | 6.1 | 19 | PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426
14 | c1avoA_ |
|  | 5.6 | 36 | PDB header:proteasome activator Chain: A: PDB Molecule:11s regulator; PDBTitle: proteasome activator reg(alpha)
15 | d1jb0k_ |
|  | 5.3 | 47 | Fold:Photosystem I reaction center subunit X, PsaK Superfamily:Photosystem I reaction center subunit X, PsaK Family:Photosystem I reaction center subunit X, PsaK

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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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