Phyre 2 Results for P0ADP9

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Email | l.a.kelley@imperial.ac.uk
Description | P0ADP9
Date | Thu Jan 5 11:21:31 GMT 2012
Unique Job ID | de76755bb9aecb1b

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2ko6A_
Top template information
PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929
Confidence and coverage
Confidence: | 100.0% | Coverage: | 100%
89 residues (100% 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 | K | C | K | R | L | N | E | V | I | E | L | L | Q | P | A | W | Q | K | E | P | D | L | N | L | L | Q | F | L | Q | K | L | A | K | E | S | G | F | D | G | E | L | A | D | L | T | D | D | I | L | I | Y | H | L | K | M | R | D | S | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | .
Sequence |  | K | D | A | V | I | P | G | L | Q | K | D | Y | E | E | D | F | K | T | A | L | L | R | A | R | G | V | I | K | E
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 |
| c2ko6A_ |

### PDB 2ko6 chain A

Region: 1 - 89
Aligned: 89
Modelled: 89
Confidence: 100.0%
Identity: 99%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein yihd;
PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929

Phyre2
2 |
| d2ibge1 |

### PDB 2ibg chain E domain 1

Region: 20 - 39
Aligned: 20
Modelled: 20
Confidence: 29.6%
Identity: 40%
Fold: Hedgehog/DD-peptidase
Superfamily: Hedgehog/DD-peptidase
Family: Hedgehog (development protein), N-terminal signaling domain

Phyre2
3 |
| d1ufwa_ |

### PDB 1ufw chain A

Region: 36 - 85
Aligned: 39
Modelled: 50
Confidence: 29.3%
Identity: 31%
Fold: Ferredoxin-like
Superfamily: RNA-binding domain, RBD
Family: Canonical RBD

Phyre2
4 |
| c3m1nB_ |

### PDB 3m1n chain B

Region: 20 - 39
Aligned: 20
Modelled: 20
Confidence: 25.7%
Identity: 40%
PDB header:signaling protein
Chain: B: PDB Molecule:sonic hedgehog protein;
PDBTitle: crystal structure of human sonic hedgehog n-terminal domain

Phyre2
5 |
| d3d1ma1 |

### PDB 3d1m chain A domain 1

Region: 20 - 39
Aligned: 20
Modelled: 20
Confidence: 24.7%
Identity: 40%
Fold: Hedgehog/DD-peptidase
Superfamily: Hedgehog/DD-peptidase
Family: Hedgehog (development protein), N-terminal signaling domain

Phyre2
6 |
| d1iasa_ |

### PDB 1ias chain A

Region: 7 - 37
Aligned: 31
Modelled: 31
Confidence: 15.6%
Identity: 19%
Fold: Protein kinase-like (PK-like)
Superfamily: Protein kinase-like (PK-like)
Family: Protein kinases, catalytic subunit

Phyre2
7 |
| c1dpuA_ |

### PDB 1dpu chain A

Region: 7 - 53
Aligned: 46
Modelled: 47
Confidence: 13.9%
Identity: 22%
PDB header:dna binding protein
Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain;
PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88)

Phyre2
8 |
| d1dpua_ |

### PDB 1dpu chain A

Region: 7 - 53
Aligned: 46
Modelled: 47
Confidence: 13.9%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: C-terminal domain of RPA32

Phyre2
9 |
| c2kxhB_ |

### PDB 2kxh chain B

Region: 74 - 86
Aligned: 13
Modelled: 13
Confidence: 10.6%
Identity: 54%
PDB header:protein binding
Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1;
PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide

Phyre2
10 |
| d2cpga_ |

### PDB 2cpg chain A

Region: 24 - 40
Aligned: 17
Modelled: 17
Confidence: 10.1%
Identity: 35%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: CopG-like

Phyre2
11 |
| d2ayxa2 |

### PDB 2ayx chain A domain 2

Region: 17 - 38
Aligned: 22
Modelled: 22
Confidence: 10.1%
Identity: 32%
Fold: Flavodoxin-like
Superfamily: CheY-like
Family: RcsC linker domain-like

Phyre2
12 |
| c1ygmA_ |

### PDB 1ygm chain A

Region: 26 - 48
Aligned: 23
Modelled: 23
Confidence: 9.1%
Identity: 39%
PDB header:membrane protein
Chain: A: PDB Molecule:hypothetical protein bsu31320;
PDBTitle: nmr structure of mistic

Phyre2
13 |
| c2noxP_ |

### PDB 2nox chain P

Region: 4 - 39
Aligned: 36
Modelled: 36
Confidence: 8.6%
Identity: 22%
PDB header:oxidoreductase
Chain: P: PDB Molecule:tryptophan 2,3-dioxygenase;
PDBTitle: crystal structure of tryptophan 2,3-dioxygenase from ralstonia2 metallidurans

Phyre2
14 |
| d1bl0a2 |

### PDB 1bl0 chain A domain 2

Region: 4 - 41
Aligned: 29
Modelled: 38
Confidence: 7.9%
Identity: 31%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2
15 |
| c3kzqE_ |

### PDB 3kzq chain E

Region: 11 - 39
Aligned: 29
Modelled: 29
Confidence: 7.7%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: E: PDB Molecule:putative uncharacterized protein vp2116;
PDBTitle: the crystal structure of the protein with unknown function from vibrio2 parahaemolyticus rimd 2210633

Phyre2
16 |
| c3db3A_ |

### PDB 3db3 chain A

Region: 48 - 65
Aligned: 18
Modelled: 18
Confidence: 7.5%
Identity: 33%
PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1;
PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide

Phyre2
17 |
| d1r4wa_ |

### PDB 1r4w chain A

Region: 9 - 44
Aligned: 36
Modelled: 36
Confidence: 7.3%
Identity: 22%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: DsbA-like

Phyre2
18 |
| d1kz7a2 |

### PDB 1kz7 chain A domain 2

Region: 36 - 53
Aligned: 16
Modelled: 16
Confidence: 7.2%
Identity: 44%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Pleckstrin-homology domain (PH domain)

Phyre2
19 |
| d1aopa4 |

### PDB 1aop chain A domain 4

Region: 4 - 47
Aligned: 44
Modelled: 44
Confidence: 6.9%
Identity: 18%
Fold: Nitrite and sulphite reductase 4Fe-4S domain-like
Superfamily: Nitrite and sulphite reductase 4Fe-4S domain-like
Family: Nitrite and sulphite reductase 4Fe-4S domain-like

Phyre2
20 |
| c2in3A_ |

### PDB 2in3 chain A

Region: 12 - 39
Aligned: 28
Modelled: 28
Confidence: 6.9%
Identity: 25%
PDB header:isomerase
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of a putative protein disulfide isomerase from2 nitrosomonas europaea

Phyre2
21 |
22 |
23 |
24 |
25 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2ko6A_ |
|  | 100.0 | 99 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929
2 | d2ibge1 |
|  | 29.6 | 40 | Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Hedgehog (development protein), N-terminal signaling domain
3 | d1ufwa_ |
|  | 29.3 | 31 | Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD
4 | c3m1nB_ |
|  | 25.7 | 40 | PDB header:signaling protein Chain: B: PDB Molecule:sonic hedgehog protein; PDBTitle: crystal structure of human sonic hedgehog n-terminal domain
5 | d3d1ma1 |
|  | 24.7 | 40 | Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Hedgehog (development protein), N-terminal signaling domain
6 | d1iasa_ |
|  | 15.6 | 19 | Fold:Protein kinase-like (PK-like) Superfamily:Protein kinase-like (PK-like) Family:Protein kinases, catalytic subunit
7 | c1dpuA_ |
|  | 13.9 | 22 | PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88)
8 | d1dpua_ |
|  | 13.9 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32
9 | c2kxhB_ |
|  | 10.6 | 54 | PDB header:protein binding Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1; PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide
10 | d2cpga_ |
|  | 10.1 | 35 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like
11 | d2ayxa2 |
|  | 10.1 | 32 | Fold:Flavodoxin-like Superfamily:CheY-like Family:RcsC linker domain-like
12 | c1ygmA_ |
|  | 9.1 | 39 | PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein bsu31320; PDBTitle: nmr structure of mistic
13 | c2noxP_ |
|  | 8.6 | 22 | PDB header:oxidoreductase Chain: P: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase from ralstonia2 metallidurans
14 | d1bl0a2 |
|  | 7.9 | 31 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator
15 | c3kzqE_ |
|  | 7.7 | 17 | PDB header:structural genomics, unknown function Chain: E: PDB Molecule:putative uncharacterized protein vp2116; PDBTitle: the crystal structure of the protein with unknown function from vibrio2 parahaemolyticus rimd 2210633
16 | c3db3A_ |
|  | 7.5 | 33 | PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide
17 | d1r4wa_ |
|  | 7.3 | 22 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbA-like
18 | d1kz7a2 |
|  | 7.2 | 44 | Fold:PH domain-like barrel Superfamily:PH domain-like Family:Pleckstrin-homology domain (PH domain)
19 | d1aopa4 |
|  | 6.9 | 18 | Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-like
20 | c2in3A_ |
|  | 6.9 | 25 | PDB header:isomerase Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative protein disulfide isomerase from2 nitrosomonas europaea
21 | c1yzxB_ |
| not modelled | 6.3 | 25 | PDB header:transferase Chain: B: PDB Molecule:glutathione s-transferase kappa 1; PDBTitle: crystal structure of human kappa class glutathione2 transferase
22 | c2nw7C_ |
| not modelled | 5.3 | 24 | PDB header:oxidoreductase Chain: C: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase (tdo) from2 xanthomonas campestris in complex with ferric heme.3 northeast structural genomics target xcr13
23 | c2htfA_ |
| not modelled | 5.2 | 50 | PDB header:transferase Chain: A: PDB Molecule:dna polymerase mu; PDBTitle: the solution structure of the brct domain from human2 polymerase reveals homology with the tdt brct domain
24 | d2ivya1 |
| not modelled | 5.1 | 21 | Fold:Ferredoxin-like Superfamily:TTP0101/SSO1404-like Family:TTP0101/SSO1404-like
25 | d1d5ya2 |
| not modelled | 5.1 | 24 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator

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