Phyre 2 Results for O13574

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | O13574
Date | Mon Jul 2 19:10:18 BST 2012
Unique Job ID | 5c1f6053afedd3eb

Summary |

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

Model (left) based on template d1sknp_
Top template information
Fold:A DNA-binding domain in eukaryotic transcription factors Superfamily:A DNA-binding domain in eukaryotic transcription factors Family:A DNA-binding domain in eukaryotic transcription factors
Confidence and coverage
Confidence: | 27.3% | Coverage: | 20%
23 residues ( 20% of your sequence) have been modelled with 27.3% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
Please note: You must be registered and logged in to use Phyrealarm.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | G | V | G | G | T | R | I | V | S | F | R | Q | P | N | Y | Y | P | V | T | Q | Q | K | G | A | S | Q | T | G | A | V | A | Q | P | Y | S | S | Y | C | G | L | L | M | R | W | A | V | V | E | I | R | R | R | G | K | G | K | G | R | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | .
Sequence |  | R | K | R | E | R | E | K | G | H | T | K | F | R | I | R | R | R | S | Y | L | Y | F | I | R | S | C | L | V | R | P | Y | S | S | G | N | K | K | N | S | C | S | F | H | K | M | L | A | I | E | I | V | L | C | L | K | A | R
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 |
| d1sknp_ |

### PDB 1skn chain P

Region: 46 - 68
Aligned: 23
Modelled: 23
Confidence: 27.3%
Identity: 43%
Fold: A DNA-binding domain in eukaryotic transcription factors
Superfamily: A DNA-binding domain in eukaryotic transcription factors
Family: A DNA-binding domain in eukaryotic transcription factors

Phyre2
2 |
| c3izcn_ |

### PDB 3izc chain N

Region: 48 - 81
Aligned: 34
Modelled: 34
Confidence: 24.1%
Identity: 38%
PDB header:ribosome
Chain: N: PDB Molecule:60s ribosomal protein rpl14 (l14e);
PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome

Phyre2
3 |
| c2kd2A_ |

### PDB 2kd2 chain A

Region: 85 - 98
Aligned: 14
Modelled: 14
Confidence: 19.1%
Identity: 36%
PDB header:apoptosis
Chain: A: PDB Molecule:fas apoptotic inhibitory molecule 1;
PDBTitle: nmr structure of faim-ctd

Phyre2
4 |
| c4a18P_ |

### PDB 4a18 chain P

Region: 67 - 81
Aligned: 15
Modelled: 15
Confidence: 17.6%
Identity: 53%
PDB header:ribosome
Chain: P: PDB Molecule:rpl38;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1

Phyre2
5 |
| c3iz5n_ |

### PDB 3iz5 chain N

Region: 48 - 81
Aligned: 32
Modelled: 34
Confidence: 17.4%
Identity: 31%
PDB header:ribosome
Chain: N: PDB Molecule:60s ribosomal protein l14 (l14e);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome

Phyre2
6 |
| c2wfuA_ |

### PDB 2wfu chain A

Region: 97 - 107
Aligned: 11
Modelled: 11
Confidence: 11.7%
Identity: 55%
PDB header:signaling protein
Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain;
PDBTitle: crystal structure of dilp5 variant db

Phyre2
7 |
| c2wfvA_ |

### PDB 2wfv chain A

Region: 97 - 107
Aligned: 11
Modelled: 11
Confidence: 11.7%
Identity: 55%
PDB header:signaling protein
Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain;
PDBTitle: crystal structure of dilp5 variant c4

Phyre2
8 |
| c2kz5A_ |

### PDB 2kz5 chain A

Region: 31 - 57
Aligned: 27
Modelled: 27
Confidence: 11.1%
Identity: 48%
PDB header:transcription
Chain: A: PDB Molecule:transcription factor nf-e2 45 kda subunit;
PDBTitle: solution nmr structure of transcription factor nf-e2 subunit's dna2 binding domain from homo sapiens, northeast structural genomics3 consortium target hr4653b

Phyre2
9 |
| c2v1lA_ |

### PDB 2v1l chain A

Region: 8 - 18
Aligned: 11
Modelled: 11
Confidence: 8.4%
Identity: 27%
PDB header:unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: structure of the conserved hypothetical protein vc1805 from2 pathogenicity island vpi-2 of vibrio cholerae o1 biovar3 eltor str. n16961 shares structural homology with the4 human p32 protein

Phyre2
10 |
| c1o7dD_ |

### PDB 1o7d chain D

Region: 13 - 21
Aligned: 9
Modelled: 9
Confidence: 7.8%
Identity: 56%
PDB header:hydrolase
Chain: D: PDB Molecule:lysosomal alpha-mannosidase;
PDBTitle: the structure of the bovine lysosomal a-mannosidase2 suggests a novel mechanism for low ph activation

Phyre2
11 |
| d1qz8a_ |

### PDB 1qz8 chain A

Region: 79 - 86
Aligned: 8
Modelled: 8
Confidence: 7.6%
Identity: 63%
Fold: Replicase NSP9
Superfamily: Replicase NSP9
Family: Replicase NSP9

Phyre2
12 |
| c2w56B_ |

### PDB 2w56 chain B

Region: 8 - 18
Aligned: 11
Modelled: 11
Confidence: 7.6%
Identity: 27%
PDB header:unknown function
Chain: B: PDB Molecule:vc0508;
PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island

Phyre2
13 |
| c2j98A_ |

### PDB 2j98 chain A

Region: 79 - 86
Aligned: 8
Modelled: 8
Confidence: 7.2%
Identity: 50%
PDB header:rna-binding protein
Chain: A: PDB Molecule:replicase polyprotein 1ab;
PDBTitle: human coronavirus 229e non structural protein 9 cys69ala2 mutant (nsp9)

Phyre2
14 |
| c1uw7A_ |

### PDB 1uw7 chain A

Region: 79 - 86
Aligned: 8
Modelled: 8
Confidence: 7.2%
Identity: 63%
PDB header:replicase protein
Chain: A: PDB Molecule:nsp9;
PDBTitle: nsp9 protein from sars-coronavirus.

Phyre2
15 |
| d2j7ja3 |

### PDB 2j7j chain A domain 3

Region: 95 - 102
Aligned: 8
Modelled: 8
Confidence: 6.6%
Identity: 63%
Fold: beta-beta-alpha zinc fingers
Superfamily: beta-beta-alpha zinc fingers
Family: Classic zinc finger, C2H2

Phyre2
16 |
| c2dzqA_ |

### PDB 2dzq chain A

Region: 9 - 17
Aligned: 9
Modelled: 9
Confidence: 6.3%
Identity: 44%
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i repeat domain-
PDBTitle: solution structure of rsgi ruh-066, a gtf2i domain in human2 cdna

Phyre2
17 |
| c3kz0D_ |

### PDB 3kz0 chain D

Region: 45 - 54
Aligned: 10
Modelled: 10
Confidence: 6.2%
Identity: 70%
PDB header:apoptosis
Chain: D: PDB Molecule:mcl-1 specific peptide mb7;
PDBTitle: mcl-1 complex with mcl-1-specific selected peptide

Phyre2
18 |
| c3kz0C_ |

### PDB 3kz0 chain C

Region: 45 - 54
Aligned: 10
Modelled: 10
Confidence: 6.2%
Identity: 70%
PDB header:apoptosis
Chain: C: PDB Molecule:mcl-1 specific peptide mb7;
PDBTitle: mcl-1 complex with mcl-1-specific selected peptide

Phyre2
19 |
| c2dn5A_ |

### PDB 2dn5 chain A

Region: 9 - 17
Aligned: 9
Modelled: 9
Confidence: 6.1%
Identity: 56%
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i repeat domain-
PDBTitle: solution structure of rsgi ruh-057, a gtf2i domain in human2 cdna

Phyre2
20 |
| c4a18A_ |

### PDB 4a18 chain A

Region: 44 - 61
Aligned: 18
Modelled: 18
Confidence: 6.1%
Identity: 39%
PDB header:ribosome
Chain: A: PDB Molecule:ribosomal protein l37;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1

Phyre2
21 |
22 |
23 |
24 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1sknp_ |
|  | 27.3 | 43 | Fold:A DNA-binding domain in eukaryotic transcription factors Superfamily:A DNA-binding domain in eukaryotic transcription factors Family:A DNA-binding domain in eukaryotic transcription factors
2 | c3izcn_ |
|  | 24.1 | 38 | PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein rpl14 (l14e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
3 | c2kd2A_ |
|  | 19.1 | 36 | PDB header:apoptosis Chain: A: PDB Molecule:fas apoptotic inhibitory molecule 1; PDBTitle: nmr structure of faim-ctd
4 | c4a18P_ |
|  | 17.6 | 53 | PDB header:ribosome Chain: P: PDB Molecule:rpl38; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1
5 | c3iz5n_ |
|  | 17.4 | 31 | PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein l14 (l14e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
6 | c2wfuA_ |
|  | 11.7 | 55 | PDB header:signaling protein Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain; PDBTitle: crystal structure of dilp5 variant db
7 | c2wfvA_ |
|  | 11.7 | 55 | PDB header:signaling protein Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain; PDBTitle: crystal structure of dilp5 variant c4
8 | c2kz5A_ |
|  | 11.1 | 48 | PDB header:transcription Chain: A: PDB Molecule:transcription factor nf-e2 45 kda subunit; PDBTitle: solution nmr structure of transcription factor nf-e2 subunit's dna2 binding domain from homo sapiens, northeast structural genomics3 consortium target hr4653b
9 | c2v1lA_ |
|  | 8.4 | 27 | PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of the conserved hypothetical protein vc1805 from2 pathogenicity island vpi-2 of vibrio cholerae o1 biovar3 eltor str. n16961 shares structural homology with the4 human p32 protein
10 | c1o7dD_ |
|  | 7.8 | 56 | PDB header:hydrolase Chain: D: PDB Molecule:lysosomal alpha-mannosidase; PDBTitle: the structure of the bovine lysosomal a-mannosidase2 suggests a novel mechanism for low ph activation
11 | d1qz8a_ |
|  | 7.6 | 63 | Fold:Replicase NSP9 Superfamily:Replicase NSP9 Family:Replicase NSP9
12 | c2w56B_ |
|  | 7.6 | 27 | PDB header:unknown function Chain: B: PDB Molecule:vc0508; PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island
13 | c2j98A_ |
|  | 7.2 | 50 | PDB header:rna-binding protein Chain: A: PDB Molecule:replicase polyprotein 1ab; PDBTitle: human coronavirus 229e non structural protein 9 cys69ala2 mutant (nsp9)
14 | c1uw7A_ |
|  | 7.2 | 63 | PDB header:replicase protein Chain: A: PDB Molecule:nsp9; PDBTitle: nsp9 protein from sars-coronavirus.
15 | d2j7ja3 |
|  | 6.6 | 63 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2
16 | c2dzqA_ |
|  | 6.3 | 44 | PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i repeat domain- PDBTitle: solution structure of rsgi ruh-066, a gtf2i domain in human2 cdna
17 | c3kz0D_ |
|  | 6.2 | 70 | PDB header:apoptosis Chain: D: PDB Molecule:mcl-1 specific peptide mb7; PDBTitle: mcl-1 complex with mcl-1-specific selected peptide
18 | c3kz0C_ |
|  | 6.2 | 70 | PDB header:apoptosis Chain: C: PDB Molecule:mcl-1 specific peptide mb7; PDBTitle: mcl-1 complex with mcl-1-specific selected peptide
19 | c2dn5A_ |
|  | 6.1 | 56 | PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i repeat domain- PDBTitle: solution structure of rsgi ruh-057, a gtf2i domain in human2 cdna
20 | c4a18A_ |
|  | 6.1 | 39 | PDB header:ribosome Chain: A: PDB Molecule:ribosomal protein l37; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1
21 | d1q60a_ |
| not modelled | 5.8 | 44 | Fold:GTF2I-like repeat Superfamily:GTF2I-like repeat Family:GTF2I-like repeat
22 | c2ed2A_ |
| not modelled | 5.8 | 44 | PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i; PDBTitle: solution structure of rsgi ruh-069, a gtf2i domain in human2 cdna
23 | c2dn4A_ |
| not modelled | 5.7 | 44 | PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i; PDBTitle: solution structure of rsgi ruh-060, a gtf2i domain in human2 cdna
24 | c2d99A_ |
| not modelled | 5.4 | 44 | PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i repeat domain- PDBTitle: solution structure of rsgi ruh-048, a gtf2i domain in human2 cdna

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