Phyre 2 Results for P0A7R5

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Email | l.a.kelley@imperial.ac.uk
Description | P0A7R5
Date | Thu Jan 5 11:06:06 GMT 2012
Unique Job ID | b5776b7bd06f9eaa

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d2qalj1
Top template information
Fold:Ferredoxin-like Superfamily:Ribosomal protein S10 Family:Ribosomal protein S10
Confidence and coverage
Confidence: | 100.0% | Coverage: | 95%
98 residues ( 95% 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 | Q | N | Q | R | I | R | I | R | L | K | A | F | D | H | R | L | I | D | Q | A | T | A | E | I | V | E | T | A | K | R | T | G | A | Q | V | R | G | P | I | P | L | P | T | R | K | E | R | F | T | V | L | I | S | P | H | V | N | K | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | .
Sequence |  | A | R | D | Q | Y | E | I | R | T | H | L | R | L | V | D | I | V | E | P | T | E | K | T | V | D | A | L | M | R | L | D | L | A | A | G | V | D | V | Q | I | S | L | G
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 |
| d2qalj1 |

### PDB 2qal chain J domain 1

Region: 5 - 102
Aligned: 98
Modelled: 98
Confidence: 100.0%
Identity: 100%
Fold: Ferredoxin-like
Superfamily: Ribosomal protein S10
Family: Ribosomal protein S10

Phyre2
2 |
| c3bbnJ_ |

### PDB 3bbn chain J

Region: 4 - 102
Aligned: 99
Modelled: 99
Confidence: 100.0%
Identity: 54%
PDB header:ribosome
Chain: J: PDB Molecule:ribosomal protein s10;
PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome.

Phyre2
3 |
| d2uubj1 |

### PDB 2uub chain J domain 1

Region: 5 - 101
Aligned: 97
Modelled: 97
Confidence: 100.0%
Identity: 55%
Fold: Ferredoxin-like
Superfamily: Ribosomal protein S10
Family: Ribosomal protein S10

Phyre2
4 |
| c2xznJ_ |

### PDB 2xzn chain J

Region: 1 - 103
Aligned: 102
Modelled: 103
Confidence: 100.0%
Identity: 28%
PDB header:ribosome
Chain: J: PDB Molecule:ribosomal protein s10 containing protein;
PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2

Phyre2
5 |
| c2zkqj_ |

### PDB 2zkq chain J

Region: 5 - 101
Aligned: 96
Modelled: 97
Confidence: 100.0%
Identity: 27%
PDB header:ribosomal protein/rna
Chain: J: PDB Molecule:
PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map

Phyre2
6 |
| c1s1hJ_ |

### PDB 1s1h chain J

Region: 5 - 100
Aligned: 95
Modelled: 96
Confidence: 100.0%
Identity: 25%
PDB header:ribosome
Chain: J: PDB Molecule:40s ribosomal protein s20;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i.

Phyre2
7 |
| c3iz6J_ |

### PDB 3iz6 chain J

Region: 2 - 102
Aligned: 100
Modelled: 100
Confidence: 100.0%
Identity: 27%
PDB header:ribosome
Chain: J: PDB Molecule:40s ribosomal protein s20 (s10p);
PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome

Phyre2
8 |
| c3r2cJ_ |

### PDB 3r2c chain J

Region: 4 - 102
Aligned: 78
Modelled: 78
Confidence: 99.9%
Identity: 55%
PDB header:transcription/rna
Chain: J: PDB Molecule:30s ribosomal protein s10;
PDBTitle: crystal structure of antitermination factors nusb and nuse in complex2 with boxa rna

Phyre2
9 |
| d1xbpg1 |

### PDB 1xbp chain G domain 1

Region: 18 - 38
Aligned: 21
Modelled: 21
Confidence: 33.6%
Identity: 29%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Ribosomal protein L11, C-terminal domain
Family: Ribosomal protein L11, C-terminal domain

Phyre2
10 |
| d1fnoa3 |

### PDB 1fno chain A domain 3

Region: 2 - 33
Aligned: 32
Modelled: 32
Confidence: 19.9%
Identity: 19%
Fold: Ferredoxin-like
Superfamily: Bacterial exopeptidase dimerisation domain
Family: Bacterial exopeptidase dimerisation domain

Phyre2
11 |
| d1hc8a_ |

### PDB 1hc8 chain A

Region: 18 - 36
Aligned: 19
Modelled: 19
Confidence: 15.5%
Identity: 37%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Ribosomal protein L11, C-terminal domain
Family: Ribosomal protein L11, C-terminal domain

Phyre2
12 |
| d1mmsa1 |

### PDB 1mms chain A domain 1

Region: 18 - 36
Aligned: 19
Modelled: 19
Confidence: 15.2%
Identity: 37%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Ribosomal protein L11, C-terminal domain
Family: Ribosomal protein L11, C-terminal domain

Phyre2
13 |
| c1s1iK_ |

### PDB 1s1i chain K

Region: 18 - 36
Aligned: 19
Modelled: 19
Confidence: 12.6%
Identity: 37%
PDB header:ribosome
Chain: K: PDB Molecule:60s ribosomal protein l12;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.

Phyre2
14 |
| c1vq8I_ |

### PDB 1vq8 chain I

Region: 18 - 36
Aligned: 19
Modelled: 19
Confidence: 11.4%
Identity: 26%
PDB header:ribosome
Chain: I: PDB Molecule:50s ribosomal protein l11p;
PDBTitle: the structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound2 to the large ribosomal subunit of haloarcula marismortui

Phyre2
15 |
| d1dbda_ |

### PDB 1dbd chain A

Region: 74 - 99
Aligned: 26
Modelled: 26
Confidence: 10.8%
Identity: 12%
Fold: Ferredoxin-like
Superfamily: Viral DNA-binding domain
Family: Viral DNA-binding domain

Phyre2
16 |
| c2kl8A_ |

### PDB 2kl8 chain A

Region: 6 - 42
Aligned: 37
Modelled: 37
Confidence: 10.3%
Identity: 22%
PDB header:de novo protein
Chain: A: PDB Molecule:or15;
PDBTitle: solution nmr structure of de novo designed ferredoxin-like2 fold protein, northeast structural genomics consortium3 target or15

Phyre2
17 |
| c2zkri_ |

### PDB 2zkr chain I

Region: 18 - 36
Aligned: 19
Modelled: 19
Confidence: 9.8%
Identity: 32%
PDB header:ribosomal protein/rna
Chain: I: PDB Molecule:rna expansion segment es15 part i;
PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map

Phyre2
18 |
| c1s6xA_ |

### PDB 1s6x chain A

Region: 46 - 56
Aligned: 11
Modelled: 11
Confidence: 9.4%
Identity: 36%
PDB header:toxin
Chain: A: PDB Molecule:kvap channel;
PDBTitle: solution structure of vstx

Phyre2
19 |
| c2yqrA_ |

### PDB 2yqr chain A

Region: 2 - 43
Aligned: 42
Modelled: 42
Confidence: 8.5%
Identity: 17%
PDB header:rna binding protein
Chain: A: PDB Molecule:kiaa0907 protein;
PDBTitle: solution structure of the kh domain in kiaa0907 protein

Phyre2
20 |
| c1jqmA_ |

### PDB 1jqm chain A

Region: 18 - 36
Aligned: 19
Modelled: 19
Confidence: 8.2%
Identity: 37%
PDB header:ribosome
Chain: A: PDB Molecule:50s ribosomal protein l11;
PDBTitle: fitting of l11 protein and elongation factor g (ef-g) in2 the cryo-em map of e. coli 70s ribosome bound with ef-g,3 gdp and fusidic acid

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2qalj1 |
|  | 100.0 | 100 | Fold:Ferredoxin-like Superfamily:Ribosomal protein S10 Family:Ribosomal protein S10
2 | c3bbnJ_ |
|  | 100.0 | 54 | PDB header:ribosome Chain: J: PDB Molecule:ribosomal protein s10; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome.
3 | d2uubj1 |
|  | 100.0 | 55 | Fold:Ferredoxin-like Superfamily:Ribosomal protein S10 Family:Ribosomal protein S10
4 | c2xznJ_ |
|  | 100.0 | 28 | PDB header:ribosome Chain: J: PDB Molecule:ribosomal protein s10 containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2
5 | c2zkqj_ |
|  | 100.0 | 27 | PDB header:ribosomal protein/rna Chain: J: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
6 | c1s1hJ_ |
|  | 100.0 | 25 | PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i.
7 | c3iz6J_ |
|  | 100.0 | 27 | PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20 (s10p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
8 | c3r2cJ_ |
|  | 99.9 | 55 | PDB header:transcription/rna Chain: J: PDB Molecule:30s ribosomal protein s10; PDBTitle: crystal structure of antitermination factors nusb and nuse in complex2 with boxa rna
9 | d1xbpg1 |
|  | 33.6 | 29 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain
10 | d1fnoa3 |
|  | 19.9 | 19 | Fold:Ferredoxin-like Superfamily:Bacterial exopeptidase dimerisation domain Family:Bacterial exopeptidase dimerisation domain
11 | d1hc8a_ |
|  | 15.5 | 37 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain
12 | d1mmsa1 |
|  | 15.2 | 37 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain
13 | c1s1iK_ |
|  | 12.6 | 37 | PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l12; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.
14 | c1vq8I_ |
|  | 11.4 | 26 | PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11p; PDBTitle: the structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound2 to the large ribosomal subunit of haloarcula marismortui
15 | d1dbda_ |
|  | 10.8 | 12 | Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain
16 | c2kl8A_ |
|  | 10.3 | 22 | PDB header:de novo protein Chain: A: PDB Molecule:or15; PDBTitle: solution nmr structure of de novo designed ferredoxin-like2 fold protein, northeast structural genomics consortium3 target or15
17 | c2zkri_ |
|  | 9.8 | 32 | PDB header:ribosomal protein/rna Chain: I: PDB Molecule:rna expansion segment es15 part i; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
18 | c1s6xA_ |
|  | 9.4 | 36 | PDB header:toxin Chain: A: PDB Molecule:kvap channel; PDBTitle: solution structure of vstx
19 | c2yqrA_ |
|  | 8.5 | 17 | PDB header:rna binding protein Chain: A: PDB Molecule:kiaa0907 protein; PDBTitle: solution structure of the kh domain in kiaa0907 protein
20 | c1jqmA_ |
|  | 8.2 | 37 | PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l11; PDBTitle: fitting of l11 protein and elongation factor g (ef-g) in2 the cryo-em map of e. coli 70s ribosome bound with ef-g,3 gdp and fusidic acid
21 | d1a7ge_ |
| not modelled | 7.8 | 16 | Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain
22 | c2vhmI_ |
| not modelled | 7.8 | 33 | PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11; PDBTitle: structure of pdf binding helix in complex with the ribosome2 (part 1 of 4)
23 | d1f9fa_ |
| not modelled | 7.7 | 8 | Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain
24 | c3izcn_ |
| not modelled | 7.6 | 24 | 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
25 | c3bboK_ |
| not modelled | 7.6 | 32 | PDB header:ribosome Chain: K: PDB Molecule:ribosomal protein l11; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome
26 | c3ai4A_ |
| not modelled | 7.3 | 20 | PDB header:fluorescent protein, replication Chain: A: PDB Molecule:yeast enhanced green fluorescent protein, dna polymerase PDBTitle: crystal structure of yeast enhanced green fluorescent protein - mouse2 polymerase iota ubiquitin binding motif fusion protein
27 | d1r8ha_ |
| not modelled | 7.1 | 8 | Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain
28 | d2q79a1 |
| not modelled | 7.1 | 15 | Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain
29 | c3lpeF_ |
| not modelled | 6.4 | 38 | PDB header:transferase Chain: F: PDB Molecule:dna-directed rna polymerase subunit e''; PDBTitle: crystal structure of spt4/5ngn heterodimer complex from methanococcus2 jannaschii
30 | d1vqoi1 |
| not modelled | 6.3 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain
31 | c2ko4A_ |
| not modelled | 6.3 | 0 | PDB header:transcription Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 15; PDBTitle: complex structure of the activation domain of gcn4 bound to the2 mediator co-activator domain of gal11/med15
32 | d1yvua2 |
| not modelled | 6.3 | 7 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:PIWI domain
33 | c2hxgB_ |
| not modelled | 6.0 | 12 | PDB header:isomerase Chain: B: PDB Molecule:l-arabinose isomerase; PDBTitle: crystal structure of mn2+ bound ecai
34 | d1iwga2 |
| not modelled | 5.8 | 15 | Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
35 | d1vqoe2 |
| not modelled | 5.4 | 17 | Fold:Ribosomal protein L6 Superfamily:Ribosomal protein L6 Family:Ribosomal protein L6
36 | c4a1eE_ |
| not modelled | 5.4 | 21 | PDB header:ribosome Chain: E: PDB Molecule:60s ribosomal protein l9; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1

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