Phyre 2 Results for P39283

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Email | l.a.kelley@imperial.ac.uk
Description | P39283
Date | Thu Jan 5 11:58:53 GMT 2012
Unique Job ID | 6ff5fb1865af2c66

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1kuta_
Top template information
Fold:SAICAR synthase-like Superfamily:SAICAR synthase-like Family:SAICAR synthase
Confidence and coverage
Confidence: | 69.7% | Coverage: | 47%
49 residues ( 47% of your sequence) have been modelled with 69.7% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | D | D | T | S | R | D | P | A | I | T | E | D | E | I | R | A | L | Q | F | S | A | G | D | V | A | E | I | E | Q | T | I | L | S | F | V | D | A | C | H | T | R | K | V | A | M | V | V | G | S | T | I | N | T | L | K | D | R | D | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | .
Sequence |  | K | R | W | G | N | L | P | D | I | Y | C | A | Y | L | I | R | C | L | V | F | R | G | E | L | V | G | Y | G | D | L | F | R | M | R | Y | S | E | I | K | R | P | V | 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 |
| d1kuta_ |

### PDB 1kut chain A

Region: 2 - 52
Aligned: 49
Modelled: 51
Confidence: 69.7%
Identity: 14%
Fold: SAICAR synthase-like
Superfamily: SAICAR synthase-like
Family: SAICAR synthase

Phyre2
2 |
| c2ywvB_ |

### PDB 2ywv chain B

Region: 2 - 52
Aligned: 49
Modelled: 51
Confidence: 65.5%
Identity: 29%
PDB header:ligase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole succinocarboxamide synthetase;
PDBTitle: crystal structure of saicar synthetase from geobacillus kaustophilus

Phyre2
3 |
| c3kreA_ |

### PDB 3kre chain A

Region: 2 - 52
Aligned: 49
Modelled: 51
Confidence: 64.2%
Identity: 20%
PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase;
PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from ehrlichia chaffeensis at 1.8a resolution

Phyre2
4 |
| c2h31A_ |

### PDB 2h31 chain A

Region: 2 - 52
Aligned: 49
Modelled: 51
Confidence: 63.0%
Identity: 22%
PDB header:ligase, lyase
Chain: A: PDB Molecule:multifunctional protein ade2;
PDBTitle: crystal structure of human paics, a bifunctional carboxylase and2 synthetase in purine biosynthesis

Phyre2
5 |
| c2gqsA_ |

### PDB 2gqs chain A

Region: 2 - 52
Aligned: 49
Modelled: 51
Confidence: 60.7%
Identity: 18%
PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide
PDBTitle: saicar synthetase complexed with cair-mg2+ and adp

Phyre2
6 |
| c2z02A_ |

### PDB 2z02 chain A

Region: 2 - 52
Aligned: 49
Modelled: 51
Confidence: 43.1%
Identity: 22%
PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide
PDBTitle: crystal structure of2 phosphoribosylaminoimidazolesuccinocarboxamide synthase3 wit atp from methanocaldococcus jannaschii

Phyre2
7 |
| c3nuaB_ |

### PDB 3nua chain B

Region: 2 - 40
Aligned: 39
Modelled: 39
Confidence: 37.1%
Identity: 15%
PDB header:ligase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase;
PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from clostridium perfringens

Phyre2
8 |
| c3dukD_ |

### PDB 3duk chain D

Region: 17 - 47
Aligned: 31
Modelled: 30
Confidence: 26.9%
Identity: 13%
PDB header:unknown function
Chain: D: PDB Molecule:ntf2-like protein of unknown function;
PDBTitle: crystal structure of a ntf2-like protein of unknown function2 (mfla_0564) from methylobacillus flagellatus kt at 2.200 a resolution

Phyre2
9 |
| c3noyA_ |

### PDB 3noy chain A

Region: 20 - 76
Aligned: 56
Modelled: 57
Confidence: 18.6%
Identity: 18%
PDB header:oxidoreductase
Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase;
PDBTitle: crystal structure of ispg (gcpe)

Phyre2
10 |
| d2rgqa1 |

### PDB 2rgq chain A domain 1

Region: 20 - 50
Aligned: 31
Modelled: 31
Confidence: 18.2%
Identity: 19%
Fold: Cystatin-like
Superfamily: NTF2-like
Family: Rv3472-like

Phyre2
11 |
| d1whra_ |

### PDB 1whr chain A

Region: 15 - 37
Aligned: 23
Modelled: 23
Confidence: 16.5%
Identity: 30%
Fold: IF3-like
Superfamily: R3H domain
Family: R3H domain

Phyre2
12 |
| c3fkaD_ |

### PDB 3fka chain D

Region: 21 - 45
Aligned: 25
Modelled: 25
Confidence: 14.7%
Identity: 12%
PDB header:unknown function
Chain: D: PDB Molecule:uncharacterized ntf-2 like protein;
PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution

Phyre2
13 |
| d1x4ta1 |

### PDB 1x4t chain A domain 1

Region: 6 - 19
Aligned: 14
Modelled: 14
Confidence: 12.5%
Identity: 29%
Fold: Long alpha-hairpin
Superfamily: ISY1 domain-like
Family: ISY1 N-terminal domain-like

Phyre2
14 |
| d1h8ba_ |

### PDB 1h8b chain A

Region: 8 - 25
Aligned: 17
Modelled: 18
Confidence: 12.3%
Identity: 24%
Fold: EF Hand-like
Superfamily: EF-hand
Family: EF-hand modules in multidomain proteins

Phyre2
15 |
| c2plyB_ |

### PDB 2ply chain B

Region: 21 - 101
Aligned: 77
Modelled: 81
Confidence: 11.2%
Identity: 14%
PDB header:translation/rna
Chain: B: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna.

Phyre2
16 |
| d1zk8a2 |

### PDB 1zk8 chain A domain 2

Region: 12 - 37
Aligned: 26
Modelled: 26
Confidence: 8.6%
Identity: 4%
Fold: Tetracyclin repressor-like, C-terminal domain
Superfamily: Tetracyclin repressor-like, C-terminal domain
Family: Tetracyclin repressor-like, C-terminal domain

Phyre2
17 |
| d1k9vf_ |

### PDB 1k9v chain F

Region: 9 - 42
Aligned: 34
Modelled: 34
Confidence: 7.4%
Identity: 21%
Fold: Flavodoxin-like
Superfamily: Class I glutamine amidotransferase-like
Family: Class I glutamine amidotransferases (GAT)

Phyre2
18 |
| d1ofcx1 |

### PDB 1ofc chain X domain 1

Region: 83 - 99
Aligned: 17
Modelled: 17
Confidence: 6.6%
Identity: 29%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Myb/SANT domain

Phyre2
19 |
| d1xlya_ |

### PDB 1xly chain A

Region: 56 - 78
Aligned: 23
Modelled: 23
Confidence: 6.5%
Identity: 4%
Fold: RNA-binding protein She2p
Superfamily: RNA-binding protein She2p
Family: RNA-binding protein She2p

Phyre2
20 |
| d1ogyb_ |

### PDB 1ogy chain B

Region: 39 - 67
Aligned: 29
Modelled: 29
Confidence: 6.5%
Identity: 28%
Fold: Multiheme cytochromes
Superfamily: Multiheme cytochromes
Family: Di-heme elbow motif

Phyre2
21 |
22 |
23 |
24 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1kuta_ |
|  | 69.7 | 14 | Fold:SAICAR synthase-like Superfamily:SAICAR synthase-like Family:SAICAR synthase
2 | c2ywvB_ |
|  | 65.5 | 29 | PDB header:ligase Chain: B: PDB Molecule:phosphoribosylaminoimidazole succinocarboxamide synthetase; PDBTitle: crystal structure of saicar synthetase from geobacillus kaustophilus
3 | c3kreA_ |
|  | 64.2 | 20 | PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase; PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from ehrlichia chaffeensis at 1.8a resolution
4 | c2h31A_ |
|  | 63.0 | 22 | PDB header:ligase, lyase Chain: A: PDB Molecule:multifunctional protein ade2; PDBTitle: crystal structure of human paics, a bifunctional carboxylase and2 synthetase in purine biosynthesis
5 | c2gqsA_ |
|  | 60.7 | 18 | PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide PDBTitle: saicar synthetase complexed with cair-mg2+ and adp
6 | c2z02A_ |
|  | 43.1 | 22 | PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide PDBTitle: crystal structure of2 phosphoribosylaminoimidazolesuccinocarboxamide synthase3 wit atp from methanocaldococcus jannaschii
7 | c3nuaB_ |
|  | 37.1 | 15 | PDB header:ligase Chain: B: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase; PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from clostridium perfringens
8 | c3dukD_ |
|  | 26.9 | 13 | PDB header:unknown function Chain: D: PDB Molecule:ntf2-like protein of unknown function; PDBTitle: crystal structure of a ntf2-like protein of unknown function2 (mfla_0564) from methylobacillus flagellatus kt at 2.200 a resolution
9 | c3noyA_ |
|  | 18.6 | 18 | PDB header:oxidoreductase Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; PDBTitle: crystal structure of ispg (gcpe)
10 | d2rgqa1 |
|  | 18.2 | 19 | Fold:Cystatin-like Superfamily:NTF2-like Family:Rv3472-like
11 | d1whra_ |
|  | 16.5 | 30 | Fold:IF3-like Superfamily:R3H domain Family:R3H domain
12 | c3fkaD_ |
|  | 14.7 | 12 | PDB header:unknown function Chain: D: PDB Molecule:uncharacterized ntf-2 like protein; PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution
13 | d1x4ta1 |
|  | 12.5 | 29 | Fold:Long alpha-hairpin Superfamily:ISY1 domain-like Family:ISY1 N-terminal domain-like
14 | d1h8ba_ |
|  | 12.3 | 24 | Fold:EF Hand-like Superfamily:EF-hand Family:EF-hand modules in multidomain proteins
15 | c2plyB_ |
|  | 11.2 | 14 | PDB header:translation/rna Chain: B: PDB Molecule:selenocysteine-specific elongation factor; PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna.
16 | d1zk8a2 |
|  | 8.6 | 4 | Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain
17 | d1k9vf_ |
|  | 7.4 | 21 | Fold:Flavodoxin-like Superfamily:Class I glutamine amidotransferase-like Family:Class I glutamine amidotransferases (GAT)
18 | d1ofcx1 |
|  | 6.6 | 29 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain
19 | d1xlya_ |
|  | 6.5 | 4 | Fold:RNA-binding protein She2p Superfamily:RNA-binding protein She2p Family:RNA-binding protein She2p
20 | d1ogyb_ |
|  | 6.5 | 28 | Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Di-heme elbow motif
21 | c2jpmA_ |
| not modelled | 6.0 | 19 | PDB header:antimicrobial protein Chain: A: PDB Molecule:bacteriocin lactococcin-g subunit beta; PDBTitle: lactococcin g-b in tfe
22 | c1y32A_ |
| not modelled | 5.8 | 71 | PDB header:unknown function Chain: A: PDB Molecule:humanin; PDBTitle: nmr structure of humanin in 30% tfe solution
23 | d1o98a1 |
| not modelled | 5.6 | 20 | Fold:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain Superfamily:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain Family:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain
24 | d1ycya1 |
| not modelled | 5.6 | 47 | Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:PF1955-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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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