Phyre 2 Results for P23862

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Email | l.a.kelley@imperial.ac.uk
Description | P23862
Date | Thu Jan 5 11:40:03 GMT 2012
Unique Job ID | 79c1ab28f9820b41

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2oszA_
Top template information
PDB header:structural protein Chain: A: PDB Molecule:nucleoporin p58/p45; PDBTitle: structure of nup58/45 suggests flexible nuclear pore diameter by2 intermolecular sliding
Confidence and coverage
Confidence: | 57.0% | Coverage: | 15%
27 residues ( 15% of your sequence) have been modelled with 57.0% 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 | K | T | A | L | L | L | E | K | L | E | G | Q | L | A | T | L | R | Q | R | C | A | P | V | S | Q | F | A | T | L | S | A | R | F | D | R | H | L | F | Q | T | R | A | T | T | L | Q | A | C | L | D | E | A | G | D | N | L | A | A | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | R | H | A | V | E | Q | Q | Q | L | P | Q | V | A | W | L | A | E | H | L | A | A | Q | L | E | A | I | A | R | E | A | S | A | W | S | L | R | E | W | D | S | A | P | P | K | I | A | R | W | Q | R | K | R | I | Q | H | Q | D | F | E | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | .
Sequence |  | R | L | R | E | M | V | A | E | R | R | A | R | L | A | R | V | T | D | L | V | E | Q | Q | T | L | H | R | E | V | E | A | Y | E | A | R | L | A | R | C | R | H | A | L | E | K | I | E | N | R | L | A | R | L | T | 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 |
| c2oszA_ |

### PDB 2osz chain A

Region: 145 - 171
Aligned: 27
Modelled: 27
Confidence: 57.0%
Identity: 33%
PDB header:structural protein
Chain: A: PDB Molecule:nucleoporin p58/p45;
PDBTitle: structure of nup58/45 suggests flexible nuclear pore diameter by2 intermolecular sliding

Phyre2
2 |
| c1ei3C_ |

### PDB 1ei3 chain C

Region: 52 - 170
Aligned: 112
Modelled: 114
Confidence: 27.9%
Identity: 10%
PDB header:
PDB COMPND:

Phyre2
3 |
| c1deqF_ |

### PDB 1deq chain F

Region: 48 - 170
Aligned: 109
Modelled: 123
Confidence: 17.6%
Identity: 9%
PDB header:
PDB COMPND:

Phyre2
4 |
| c3ojaB_ |

### PDB 3oja chain B

Region: 40 - 174
Aligned: 130
Modelled: 130
Confidence: 17.0%
Identity: 16%
PDB header:protein binding
Chain: B: PDB Molecule:anopheles plasmodium-responsive leucine-rich repeat protein
PDBTitle: crystal structure of lrim1/apl1c complex

Phyre2
5 |
| c3u59C_ |

### PDB 3u59 chain C

Region: 77 - 174
Aligned: 95
Modelled: 98
Confidence: 15.3%
Identity: 7%
PDB header:contractile protein
Chain: C: PDB Molecule:tropomyosin beta chain;
PDBTitle: n-terminal 98-aa fragment of smooth muscle tropomyosin beta

Phyre2
6 |
| c1deqO_ |

### PDB 1deq chain O

Region: 110 - 174
Aligned: 63
Modelled: 65
Confidence: 14.4%
Identity: 11%
PDB header:
PDB COMPND:

Phyre2
7 |
| c2wukD_ |

### PDB 2wuk chain D

Region: 23 - 70
Aligned: 48
Modelled: 48
Confidence: 14.3%
Identity: 6%
PDB header:cell cycle
Chain: D: PDB Molecule:septum site-determining protein diviva;
PDBTitle: diviva n-terminal domain, f17a mutant

Phyre2
8 |
| c2xusA_ |

### PDB 2xus chain A

Region: 153 - 173
Aligned: 21
Modelled: 21
Confidence: 13.5%
Identity: 24%
PDB header:protein binding
Chain: A: PDB Molecule:breast cancer metastasis-suppressor 1;
PDBTitle: crystal structure of the brms1 n-terminal region

Phyre2
9 |
| d1k1fa_ |

### PDB 1k1f chain A

Region: 149 - 172
Aligned: 24
Modelled: 24
Confidence: 13.0%
Identity: 21%
Fold: Bcr-Abl oncoprotein oligomerization domain
Superfamily: Bcr-Abl oncoprotein oligomerization domain
Family: Bcr-Abl oncoprotein oligomerization domain

Phyre2
10 |
| c3cwgA_ |

### PDB 3cwg chain A

Region: 41 - 175
Aligned: 129
Modelled: 135
Confidence: 10.9%
Identity: 7%
PDB header:transcription
Chain: A: PDB Molecule:signal transducer and activator of transcription
PDBTitle: unphosphorylated mouse stat3 core fragment

Phyre2
11 |
| c2efrB_ |

### PDB 2efr chain B

Region: 7 - 175
Aligned: 151
Modelled: 154
Confidence: 10.3%
Identity: 11%
PDB header:contractile protein
Chain: B: PDB Molecule:general control protein gcn4 and tropomyosin 1 alpha chain;
PDBTitle: crystal structure of the c-terminal tropomyosin fragment with n- and2 c-terminal extensions of the leucine zipper at 1.8 angstroms3 resolution

Phyre2
12 |
| c3pltB_ |

### PDB 3plt chain B

Region: 78 - 175
Aligned: 94
Modelled: 98
Confidence: 10.2%
Identity: 14%
PDB header:structural protein
Chain: B: PDB Molecule:sphingolipid long chain base-responsive protein lsp1;
PDBTitle: crystal structure of lsp1 from saccharomyces cerevisiae

Phyre2
13 |
| c2gl2B_ |

### PDB 2gl2 chain B

Region: 79 - 174
Aligned: 93
Modelled: 96
Confidence: 9.2%
Identity: 13%
PDB header:cell adhesion
Chain: B: PDB Molecule:adhesion a;
PDBTitle: crystal structure of the tetra muntant (t66g,r67g,f68g,2 y69g) of bacterial adhesin fada

Phyre2
14 |
| d2gtsa1 |

### PDB 2gts chain A domain 1

Region: 7 - 52
Aligned: 46
Modelled: 46
Confidence: 7.7%
Identity: 24%
Fold: Ferritin-like
Superfamily: HP0062-like
Family: HP0062-like

Phyre2
15 |
| d1ykhb1 |

### PDB 1ykh chain B domain 1

Region: 40 - 139
Aligned: 96
Modelled: 100
Confidence: 6.2%
Identity: 13%
Fold: Mediator hinge subcomplex-like
Superfamily: Mediator hinge subcomplex-like
Family: CSE2-like

Phyre2
16 |
| c2x6pB_ |

### PDB 2x6p chain B

Region: 143 - 167
Aligned: 25
Modelled: 25
Confidence: 5.9%
Identity: 32%
PDB header:de novo protein
Chain: B: PDB Molecule:coil ser l19c;
PDBTitle: crystal structure of coil ser l19c

Phyre2
17 |
| c2x6pA_ |

### PDB 2x6p chain A

Region: 143 - 167
Aligned: 25
Modelled: 25
Confidence: 5.9%
Identity: 32%
PDB header:de novo protein
Chain: A: PDB Molecule:coil ser l19c;
PDBTitle: crystal structure of coil ser l19c

Phyre2
18 |
| d1sdia_ |

### PDB 1sdi chain A

Region: 1 - 49
Aligned: 46
Modelled: 46
Confidence: 5.7%
Identity: 9%
Fold: YcfC-like
Superfamily: YcfC-like
Family: YcfC-like

Phyre2
19 |
| c2x6pC_ |

### PDB 2x6p chain C

Region: 143 - 168
Aligned: 26
Modelled: 26
Confidence: 5.5%
Identity: 31%
PDB header:de novo protein
Chain: C: PDB Molecule:coil ser l19c;
PDBTitle: crystal structure of coil ser l19c

Phyre2
20 |
| d1gs9a_ |

### PDB 1gs9 chain A

Region: 5 - 134
Aligned: 129
Modelled: 130
Confidence: 5.3%
Identity: 15%
Fold: Four-helical up-and-down bundle
Superfamily: Apolipoprotein
Family: Apolipoprotein

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2oszA_ |
|  | 57.0 | 33 | PDB header:structural protein Chain: A: PDB Molecule:nucleoporin p58/p45; PDBTitle: structure of nup58/45 suggests flexible nuclear pore diameter by2 intermolecular sliding
2 | c1ei3C_ |
|  | 27.9 | 10 | PDB header: PDB COMPND:
3 | c1deqF_ |
|  | 17.6 | 9 | PDB header: PDB COMPND:
4 | c3ojaB_ |
|  | 17.0 | 16 | PDB header:protein binding Chain: B: PDB Molecule:anopheles plasmodium-responsive leucine-rich repeat protein PDBTitle: crystal structure of lrim1/apl1c complex
5 | c3u59C_ |
|  | 15.3 | 7 | PDB header:contractile protein Chain: C: PDB Molecule:tropomyosin beta chain; PDBTitle: n-terminal 98-aa fragment of smooth muscle tropomyosin beta
6 | c1deqO_ |
|  | 14.4 | 11 | PDB header: PDB COMPND:
7 | c2wukD_ |
|  | 14.3 | 6 | PDB header:cell cycle Chain: D: PDB Molecule:septum site-determining protein diviva; PDBTitle: diviva n-terminal domain, f17a mutant
8 | c2xusA_ |
|  | 13.5 | 24 | PDB header:protein binding Chain: A: PDB Molecule:breast cancer metastasis-suppressor 1; PDBTitle: crystal structure of the brms1 n-terminal region
9 | d1k1fa_ |
|  | 13.0 | 21 | Fold:Bcr-Abl oncoprotein oligomerization domain Superfamily:Bcr-Abl oncoprotein oligomerization domain Family:Bcr-Abl oncoprotein oligomerization domain
10 | c3cwgA_ |
|  | 10.9 | 7 | PDB header:transcription Chain: A: PDB Molecule:signal transducer and activator of transcription PDBTitle: unphosphorylated mouse stat3 core fragment
11 | c2efrB_ |
|  | 10.3 | 11 | PDB header:contractile protein Chain: B: PDB Molecule:general control protein gcn4 and tropomyosin 1 alpha chain; PDBTitle: crystal structure of the c-terminal tropomyosin fragment with n- and2 c-terminal extensions of the leucine zipper at 1.8 angstroms3 resolution
12 | c3pltB_ |
|  | 10.2 | 14 | PDB header:structural protein Chain: B: PDB Molecule:sphingolipid long chain base-responsive protein lsp1; PDBTitle: crystal structure of lsp1 from saccharomyces cerevisiae
13 | c2gl2B_ |
|  | 9.2 | 13 | PDB header:cell adhesion Chain: B: PDB Molecule:adhesion a; PDBTitle: crystal structure of the tetra muntant (t66g,r67g,f68g,2 y69g) of bacterial adhesin fada
14 | d2gtsa1 |
|  | 7.7 | 24 | Fold:Ferritin-like Superfamily:HP0062-like Family:HP0062-like
15 | d1ykhb1 |
|  | 6.2 | 13 | Fold:Mediator hinge subcomplex-like Superfamily:Mediator hinge subcomplex-like Family:CSE2-like
16 | c2x6pB_ |
|  | 5.9 | 32 | PDB header:de novo protein Chain: B: PDB Molecule:coil ser l19c; PDBTitle: crystal structure of coil ser l19c
17 | c2x6pA_ |
|  | 5.9 | 32 | PDB header:de novo protein Chain: A: PDB Molecule:coil ser l19c; PDBTitle: crystal structure of coil ser l19c
18 | d1sdia_ |
|  | 5.7 | 9 | Fold:YcfC-like Superfamily:YcfC-like Family:YcfC-like
19 | c2x6pC_ |
|  | 5.5 | 31 | PDB header:de novo protein Chain: C: PDB Molecule:coil ser l19c; PDBTitle: crystal structure of coil ser l19c
20 | d1gs9a_ |
|  | 5.3 | 15 | Fold:Four-helical up-and-down bundle Superfamily:Apolipoprotein Family:Apolipoprotein

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