Phyre 2 Results for Q9XB42

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Email | l.a.kelley@imperial.ac.uk
Description | Q9XB42
Date | Thu Jan 5 12:38:30 GMT 2012
Unique Job ID | ddd3c13c5b1f0cd8

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d2cqma1
Top template information
Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
Confidence and coverage
Confidence: | 58.6% | Coverage: | 41%
30 residues ( 41% of your sequence) have been modelled with 58.6% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | K | I | I | S | K | R | R | A | M | T | I | Y | R | Q | H | P | E | S | R | I | F | R | Y | C | T | G | K | Y | Q | W | H | G | S | V | C | H | Y | T | G | R | D | V | P | D | I | A | G | V | L | A | V | Y | A | E | R | R | Q | D | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | .
Sequence |  | N | G | P | Y | T | C | L | M | S | I | T | L | N
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 |
| d2cqma1 |

### PDB 2cqm chain A domain 1

Region: 41 - 70
Aligned: 30
Modelled: 30
Confidence: 58.6%
Identity: 30%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
2 |
| d1gd8a_ |

### PDB 1gd8 chain A

Region: 41 - 70
Aligned: 30
Modelled: 30
Confidence: 53.1%
Identity: 30%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
3 |
| d2zjrk1 |

### PDB 2zjr chain K domain 1

Region: 41 - 68
Aligned: 28
Modelled: 28
Confidence: 53.1%
Identity: 25%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
4 |
| c3bboP_ |

### PDB 3bbo chain P

Region: 41 - 68
Aligned: 28
Modelled: 28
Confidence: 34.8%
Identity: 25%
PDB header:ribosome
Chain: P: PDB Molecule:ribosomal protein l17;
PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome

Phyre2
5 |
| d2qamn1 |

### PDB 2qam chain N domain 1

Region: 41 - 68
Aligned: 28
Modelled: 28
Confidence: 30.5%
Identity: 29%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
6 |
| d1bnla_ |

### PDB 1bnl chain A

Region: 6 - 39
Aligned: 34
Modelled: 34
Confidence: 15.5%
Identity: 18%
Fold: C-type lectin-like
Superfamily: C-type lectin-like
Family: Endostatin

Phyre2
7 |
| c2qh7A_ |

### PDB 2qh7 chain A

Region: 18 - 27
Aligned: 10
Modelled: 10
Confidence: 12.3%
Identity: 40%
PDB header:metal binding protein
Chain: A: PDB Molecule:zinc finger cdgsh-type domain 1;
PDBTitle: mitoneet is a uniquely folded 2fe-2s outer mitochondrial membrane2 protein stabilized by pioglitazone

Phyre2
8 |
| c3fnvB_ |

### PDB 3fnv chain B

Region: 18 - 27
Aligned: 10
Modelled: 10
Confidence: 12.3%
Identity: 40%
PDB header:metal binding protein
Chain: B: PDB Molecule:cdgsh iron sulfur domain-containing protein 2;
PDBTitle: crystal structure of miner1: the redox-active 2fe-2s protein causative2 in wolfram syndrome 2

Phyre2
9 |
| c2gyrB_ |

### PDB 2gyr chain B

Region: 16 - 28
Aligned: 13
Modelled: 13
Confidence: 11.2%
Identity: 38%
PDB header:hormone/growth factor
Chain: B: PDB Molecule:neurotrophic factor artemin, isoform 3;
PDBTitle: crystal structure of human artemin

Phyre2
10 |
| d1ir1s_ |

### PDB 1ir1 chain S

Region: 31 - 70
Aligned: 40
Modelled: 40
Confidence: 11.1%
Identity: 25%
Fold: RuBisCO, small subunit
Superfamily: RuBisCO, small subunit
Family: RuBisCO, small subunit

Phyre2
11 |
| d2j7qa1 |

### PDB 2j7q chain A domain 1

Region: 1 - 59
Aligned: 48
Modelled: 59
Confidence: 8.7%
Identity: 19%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: M48USP-like

Phyre2
12 |
| c3fkaD_ |

### PDB 3fka chain D

Region: 16 - 72
Aligned: 45
Modelled: 57
Confidence: 8.5%
Identity: 13%
PDB header:unknown function
Chain: D: PDB Molecule:uncharacterized ntf-2 like protein;
PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution

Phyre2
13 |
| d1koea_ |

### PDB 1koe chain A

Region: 8 - 39
Aligned: 32
Modelled: 32
Confidence: 8.4%
Identity: 19%
Fold: C-type lectin-like
Superfamily: C-type lectin-like
Family: Endostatin

Phyre2
14 |
| d1ztxe1 |

### PDB 1ztx chain E domain 1

Region: 21 - 37
Aligned: 17
Modelled: 17
Confidence: 8.2%
Identity: 12%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: E set domains
Family: Class II viral fusion proteins C-terminal domain

Phyre2
15 |
| c2wsfN_ |

### PDB 2wsf chain N

Region: 6 - 61
Aligned: 55
Modelled: 56
Confidence: 7.3%
Identity: 20%
PDB header:photosynthesis
Chain: N: PDB Molecule:photosystem i-n subunit;
PDBTitle: improved model of plant photosystem i

Phyre2
16 |
| c3egpA_ |

### PDB 3egp chain A

Region: 21 - 32
Aligned: 12
Modelled: 12
Confidence: 7.3%
Identity: 25%
PDB header:viral protein
Chain: A: PDB Molecule:envelope protein;
PDBTitle: crystal structure analysis of dengue-1 envelope protein2 domain iii

Phyre2
17 |
| d1ok8a1 |

### PDB 1ok8 chain A domain 1

Region: 21 - 37
Aligned: 17
Modelled: 17
Confidence: 6.8%
Identity: 24%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: E set domains
Family: Class II viral fusion proteins C-terminal domain

Phyre2
18 |
| c2kztA_ |

### PDB 2kzt chain A

Region: 42 - 56
Aligned: 15
Modelled: 15
Confidence: 6.7%
Identity: 20%
PDB header:apoptosis
Chain: A: PDB Molecule:programmed cell death protein 4;
PDBTitle: structure of the tandem ma-3 region of pdcd4

Phyre2
19 |
| d1hd2a_ |

### PDB 1hd2 chain A

Region: 27 - 51
Aligned: 25
Modelled: 25
Confidence: 6.6%
Identity: 12%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: Glutathione peroxidase-like

Phyre2
20 |
| c2o01N_ |

### PDB 2o01 chain N

Region: 6 - 61
Aligned: 55
Modelled: 56
Confidence: 5.9%
Identity: 20%
PDB header:photosynthesis
Chain: N: PDB Molecule:photosystem i-n subunit;
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2cqma1 |
|  | 58.6 | 30 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
2 | d1gd8a_ |
|  | 53.1 | 30 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
3 | d2zjrk1 |
|  | 53.1 | 25 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
4 | c3bboP_ |
|  | 34.8 | 25 | PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein l17; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome
5 | d2qamn1 |
|  | 30.5 | 29 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
6 | d1bnla_ |
|  | 15.5 | 18 | Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Endostatin
7 | c2qh7A_ |
|  | 12.3 | 40 | PDB header:metal binding protein Chain: A: PDB Molecule:zinc finger cdgsh-type domain 1; PDBTitle: mitoneet is a uniquely folded 2fe-2s outer mitochondrial membrane2 protein stabilized by pioglitazone
8 | c3fnvB_ |
|  | 12.3 | 40 | PDB header:metal binding protein Chain: B: PDB Molecule:cdgsh iron sulfur domain-containing protein 2; PDBTitle: crystal structure of miner1: the redox-active 2fe-2s protein causative2 in wolfram syndrome 2
9 | c2gyrB_ |
|  | 11.2 | 38 | PDB header:hormone/growth factor Chain: B: PDB Molecule:neurotrophic factor artemin, isoform 3; PDBTitle: crystal structure of human artemin
10 | d1ir1s_ |
|  | 11.1 | 25 | Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit
11 | d2j7qa1 |
|  | 8.7 | 19 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:M48USP-like
12 | c3fkaD_ |
|  | 8.5 | 13 | PDB header:unknown function Chain: D: PDB Molecule:uncharacterized ntf-2 like protein; PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution
13 | d1koea_ |
|  | 8.4 | 19 | Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Endostatin
14 | d1ztxe1 |
|  | 8.2 | 12 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain
15 | c2wsfN_ |
|  | 7.3 | 20 | PDB header:photosynthesis Chain: N: PDB Molecule:photosystem i-n subunit; PDBTitle: improved model of plant photosystem i
16 | c3egpA_ |
|  | 7.3 | 25 | PDB header:viral protein Chain: A: PDB Molecule:envelope protein; PDBTitle: crystal structure analysis of dengue-1 envelope protein2 domain iii
17 | d1ok8a1 |
|  | 6.8 | 24 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain
18 | c2kztA_ |
|  | 6.7 | 20 | PDB header:apoptosis Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: structure of the tandem ma-3 region of pdcd4
19 | d1hd2a_ |
|  | 6.6 | 12 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like
20 | c2o01N_ |
|  | 5.9 | 20 | PDB header:photosynthesis Chain: N: PDB Molecule:photosystem i-n subunit; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
21 | c2riqA_ |
| not modelled | 5.9 | 15 | PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: crystal structure of the third zinc-binding domain of human parp-1
22 | d2j01s1 |
| not modelled | 5.7 | 33 | Fold:Ribonuclease H-like motif Superfamily:Translational machinery components Family:Ribosomal protein L18 and S11
23 | c3ccjU_ |
| not modelled | 5.7 | 23 | PDB header:ribosome Chain: U: PDB Molecule:50s ribosomal protein l24e; PDBTitle: structure of anisomycin resistant 50s ribosomal subunit: 23s rrna2 mutation c2534u
24 | d1vqou1 |
| not modelled | 5.6 | 23 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Ribosomal protein L24e
25 | c2iosA_ |
| not modelled | 5.5 | 40 | PDB header:antitumor protein Chain: A: PDB Molecule:programmed cell death 4, pdcd4; PDBTitle: crystal structure of the c-terminal ma3 domain of pdcd42 (mouse); form 3
26 | c2rg8A_ |
| not modelled | 5.5 | 20 | PDB header:apoptosis, translation Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: crystal structure of programmed for cell death 4 middle ma32 domain
27 | d1m9sa3 |
| not modelled | 5.4 | 18 | Fold:SH3-like barrel Superfamily:Prokaryotic SH3-related domain Family:GW domain
28 | c2h0pA_ |
| not modelled | 5.2 | 18 | PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein; PDBTitle: nmr structure of the dengue-4 virus envelope protein domain2 iii
29 | c3oe3B_ |
| not modelled | 5.1 | 16 | PDB header:hydrolase inhibitor Chain: B: PDB Molecule:putative periplasmic protein; PDBTitle: crystal structure of plic-st, periplasmic lysozyme inhibitor of c-type2 lysozyme from salmonella typhimurium
30 | d1pjwa_ |
| not modelled | 5.1 | 18 | Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain
31 | c2jqmA_ |
| not modelled | 5.1 | 18 | PDB header:transferase Chain: A: PDB Molecule:envelope protein e; PDBTitle: yellow fever envelope protein domain iii nmr structure2 (s288-k398)

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