Phyre 2 Results for P0A0I4

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Email | l.a.kelley@imperial.ac.uk
Description | P0A0I4
Date | Tue Jul 17 17:05:06 BST 2012
Unique Job ID | d62902ff64f127ca

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2akhZ_
Top template information
PDB header:protein transport Chain: Z: PDB Molecule:preprotein translocase sece subunit; PDBTitle: normal mode-based flexible fitted coordinates of a non-2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli
Confidence and coverage
Confidence: | 99.8% | Coverage: | 97%
58 residues ( 97% of your sequence) have been modelled with 99.8% 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 | A | K | K | E | S | F | F | K | G | V | K | S | E | M | E | K | T | S | W | P | T | K | E | E | L | F | K | Y | T | V | I | V | V | S | T | V | I | F | F | L | V | F | F | Y | A | L | D | L | G | I | T | A | L | K | N | L | L | F | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
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Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Sequence |
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 |
| c2akhZ_ |

### PDB 2akh chain Z

Region: 3 - 60
Aligned: 58
Modelled: 58
Confidence: 99.8%
Identity: 24%
PDB header:protein transport
Chain: Z: PDB Molecule:preprotein translocase sece subunit;
PDBTitle: normal mode-based flexible fitted coordinates of a non-2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli

Phyre2
2 |
| c3dinD_ |

### PDB 3din chain D

Region: 10 - 60
Aligned: 51
Modelled: 51
Confidence: 99.8%
Identity: 27%
PDB header:membrane protein, protein transport
Chain: D: PDB Molecule:preprotein translocase subunit sece;
PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase

Phyre2
3 |
| c2zjsE_ |

### PDB 2zjs chain E

Region: 12 - 56
Aligned: 45
Modelled: 45
Confidence: 98.9%
Identity: 22%
PDB header:protein transport/immune system
Chain: E: PDB Molecule:preprotein translocase sece subunit;
PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment

Phyre2
4 |
| c3dl8D_ |

### PDB 3dl8 chain D

Region: 28 - 60
Aligned: 33
Modelled: 33
Confidence: 96.9%
Identity: 24%
PDB header:protein transport
Chain: D: PDB Molecule:sece;
PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca

Phyre2
5 |
| d1rhzb_ |

### PDB 1rhz chain B

Region: 2 - 58
Aligned: 57
Modelled: 57
Confidence: 94.4%
Identity: 16%
Fold: Single transmembrane helix
Superfamily: Preprotein translocase SecE subunit
Family: Preprotein translocase SecE subunit

Phyre2
6 |
| c2wwbB_ |

### PDB 2wwb chain B

Region: 1 - 60
Aligned: 60
Modelled: 60
Confidence: 93.9%
Identity: 13%
PDB header:ribosome
Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma;
PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome

Phyre2
7 |
| c2ww9B_ |

### PDB 2ww9 chain B

Region: 1 - 58
Aligned: 58
Modelled: 58
Confidence: 93.4%
Identity: 17%
PDB header:ribosome
Chain: B: PDB Molecule:protein transport protein sss1;
PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome

Phyre2
8 |
| d1rh5b_ |

### PDB 1rh5 chain B

Region: 5 - 58
Aligned: 54
Modelled: 54
Confidence: 70.9%
Identity: 17%
Fold: Single transmembrane helix
Superfamily: Preprotein translocase SecE subunit
Family: Preprotein translocase SecE subunit

Phyre2
9 |
| c3mp7B_ |

### PDB 3mp7 chain B

Region: 4 - 51
Aligned: 48
Modelled: 48
Confidence: 61.4%
Identity: 17%
PDB header:protein transport
Chain: B: PDB Molecule:preprotein translocase subunit sece;
PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes

Phyre2
10 |
| c1yq3C_ |

### PDB 1yq3 chain C

Region: 22 - 47
Aligned: 26
Modelled: 26
Confidence: 28.6%
Identity: 12%
PDB header:oxidoreductase
Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit;
PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone

Phyre2
11 |
| c2ehbD_ |

### PDB 2ehb chain D

Region: 5 - 20
Aligned: 16
Modelled: 16
Confidence: 15.6%
Identity: 31%
PDB header:signalling protein/transferase
Chain: D: PDB Molecule:cbl-interacting serine/threonine-protein kinase 24;
PDBTitle: the structure of the c-terminal domain of the protein kinase atsos22 bound to the calcium sensor atsos3

Phyre2
12 |
| d1v0da_ |

### PDB 1v0d chain A

Region: 2 - 28
Aligned: 27
Modelled: 27
Confidence: 14.3%
Identity: 11%
Fold: His-Me finger endonucleases
Superfamily: His-Me finger endonucleases
Family: Caspase-activated DNase, CAD (DffB, DFF40)

Phyre2
13 |
| c1v0dA_ |

### PDB 1v0d chain A

Region: 2 - 28
Aligned: 27
Modelled: 27
Confidence: 14.3%
Identity: 11%
PDB header:hydrolase
Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit;
PDBTitle: crystal structure of caspase-activated dnase (cad)

Phyre2
14 |
| c3fwbB_ |

### PDB 3fwb chain B

Region: 2 - 24
Aligned: 23
Modelled: 23
Confidence: 12.4%
Identity: 13%
PDB header:cell cycle, transcription
Chain: B: PDB Molecule:nuclear mrna export protein sac3;
PDBTitle: sac3:sus1:cdc31 complex

Phyre2
15 |
| d1qopa_ |

### PDB 1qop chain A

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 11.6%
Identity: 24%
Fold: TIM beta/alpha-barrel
Superfamily: Ribulose-phoshate binding barrel
Family: Tryptophan biosynthesis enzymes

Phyre2
16 |
| d1jy1a2 |

### PDB 1jy1 chain A domain 2

Region: 17 - 29
Aligned: 13
Modelled: 13
Confidence: 11.2%
Identity: 15%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Tyrosyl-DNA phosphodiesterase TDP1

Phyre2
17 |
| c2ekcA_ |

### PDB 2ekc chain A

Region: 1 - 29
Aligned: 29
Modelled: 28
Confidence: 8.9%
Identity: 31%
PDB header:lyase
Chain: A: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: structural study of project id aq_1548 from aquifex aeolicus vf5

Phyre2
18 |
| d1xcfa_ |

### PDB 1xcf chain A

Region: 1 - 28
Aligned: 28
Modelled: 28
Confidence: 8.3%
Identity: 32%
Fold: TIM beta/alpha-barrel
Superfamily: Ribulose-phoshate binding barrel
Family: Tryptophan biosynthesis enzymes

Phyre2
19 |
| c3sq3C_ |

### PDB 3sq3 chain C

Region: 17 - 29
Aligned: 13
Modelled: 13
Confidence: 8.0%
Identity: 23%
PDB header:hydrolase
Chain: C: PDB Molecule:tyrosyl-dna phosphodiesterase 1;
PDBTitle: crystal structure analysis of the yeast tyrosyl-dna phosphodiesterase2 h182a mutant

Phyre2
20 |
| c2yskA_ |

### PDB 2ysk chain A

Region: 2 - 34
Aligned: 30
Modelled: 33
Confidence: 7.8%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein ttha1432;
PDBTitle: crystal structure of a hypothetical protein ttha1432 from thermus2 thermophilus

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2akhZ_ |
|  | 99.8 | 24 | PDB header:protein transport Chain: Z: PDB Molecule:preprotein translocase sece subunit; PDBTitle: normal mode-based flexible fitted coordinates of a non-2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli
2 | c3dinD_ |
|  | 99.8 | 27 | PDB header:membrane protein, protein transport Chain: D: PDB Molecule:preprotein translocase subunit sece; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase
3 | c2zjsE_ |
|  | 98.9 | 22 | PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment
4 | c3dl8D_ |
|  | 96.9 | 24 | PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca
5 | d1rhzb_ |
|  | 94.4 | 16 | Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit
6 | c2wwbB_ |
|  | 93.9 | 13 | PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome
7 | c2ww9B_ |
|  | 93.4 | 17 | PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome
8 | d1rh5b_ |
|  | 70.9 | 17 | Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit
9 | c3mp7B_ |
|  | 61.4 | 17 | PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes
10 | c1yq3C_ |
|  | 28.6 | 12 | PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone
11 | c2ehbD_ |
|  | 15.6 | 31 | PDB header:signalling protein/transferase Chain: D: PDB Molecule:cbl-interacting serine/threonine-protein kinase 24; PDBTitle: the structure of the c-terminal domain of the protein kinase atsos22 bound to the calcium sensor atsos3
12 | d1v0da_ |
|  | 14.3 | 11 | Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:Caspase-activated DNase, CAD (DffB, DFF40)
13 | c1v0dA_ |
|  | 14.3 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad)
14 | c3fwbB_ |
|  | 12.4 | 13 | PDB header:cell cycle, transcription Chain: B: PDB Molecule:nuclear mrna export protein sac3; PDBTitle: sac3:sus1:cdc31 complex
15 | d1qopa_ |
|  | 11.6 | 24 | Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:Tryptophan biosynthesis enzymes
16 | d1jy1a2 |
|  | 11.2 | 15 | Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:Tyrosyl-DNA phosphodiesterase TDP1
17 | c2ekcA_ |
|  | 8.9 | 31 | PDB header:lyase Chain: A: PDB Molecule:tryptophan synthase alpha chain; PDBTitle: structural study of project id aq_1548 from aquifex aeolicus vf5
18 | d1xcfa_ |
|  | 8.3 | 32 | Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:Tryptophan biosynthesis enzymes
19 | c3sq3C_ |
|  | 8.0 | 23 | PDB header:hydrolase Chain: C: PDB Molecule:tyrosyl-dna phosphodiesterase 1; PDBTitle: crystal structure analysis of the yeast tyrosyl-dna phosphodiesterase2 h182a mutant
20 | c2yskA_ |
|  | 7.8 | 13 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha1432; PDBTitle: crystal structure of a hypothetical protein ttha1432 from thermus2 thermophilus
21 | d1k8ke_ |
| not modelled | 7.5 | 6 | Fold:Arp2/3 complex 21 kDa subunit ARPC3 Superfamily:Arp2/3 complex 21 kDa subunit ARPC3 Family:Arp2/3 complex 21 kDa subunit ARPC3
22 | d1q32a2 |
| not modelled | 7.4 | 23 | Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:Tyrosyl-DNA phosphodiesterase TDP1
23 | c3vrbG_ |
| not modelled | 6.8 | 4 | PDB header:oxidoreductase/oxidoreductase inhibitor Chain: G: PDB Molecule:cytochrome b-large subunit; PDBTitle: mitochondrial rhodoquinol-fumarate reductase from the parasitic2 nematode ascaris suum with the specific inhibitor flutolanil and3 substrate fumarate
24 | d2okqa1 |
| not modelled | 6.7 | 38 | Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:YbaA-like
25 | c2wmhA_ |
| not modelled | 6.7 | 43 | PDB header:hydrolase Chain: A: PDB Molecule:fucolectin-related protein; PDBTitle: crystal structure of the catalytic module of a family 982 glycoside hydrolase from streptococcus pneumoniae tigr4 in3 complex with the h-disaccharide blood group antigen.
26 | c1nopB_ |
| not modelled | 6.4 | 15 | PDB header:hydrolase/dna Chain: B: PDB Molecule:tyrosyl-dna phosphodiesterase 1; PDBTitle: crystal structure of human tyrosyl-dna phosphodiesterase2 (tdp1) in complex with vanadate, dna and a human3 topoisomerase i-derived peptide

Binding site prediction |

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