Phyre 2 Results for P0AG44

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Email | l.a.kelley@imperial.ac.uk
Description | P0AG44
Date | Thu Jan 5 11:28:06 GMT 2012
Unique Job ID | a28d3a57cc86abdf

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d2qamn1
Top template information
Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
Confidence and coverage
Confidence: | 100.0% | Coverage: | 94%
120 residues ( 94% 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 |

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Sequence |  | M | R | H | R | K | S | G | R | Q | L | N | R | N | S | S | H | R | Q | A | M | F | R | N | M | A | G | S | L | V | R | H | E | I | I | K | T | T | L | P | K | A | K | E | L | R | R | V | V | E | P | L | I | T | L | A | K | T | D | S | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | A | N | R | R | L | A | F | A | R | T | R | D | N | E | I | V | A | K | L | F | N | E | L | G | P | R | F | A | S | R | A | G | G | Y | T | R | I | L | K | C | G | F | R | A | G | D | N | A | P | M | A | Y | I | E | L | V | D | R | S | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | .
Sequence |  | K | A | E | A | A | A | E
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 |
| d2qamn1 |

### PDB 2qam chain N domain 1

Region: 1 - 120
Aligned: 120
Modelled: 120
Confidence: 100.0%
Identity: 100%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
2 |
| c3bboP_ |

### PDB 3bbo chain P

Region: 1 - 116
Aligned: 116
Modelled: 116
Confidence: 100.0%
Identity: 45%
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
3 |
| d2zjrk1 |

### PDB 2zjr chain K domain 1

Region: 3 - 115
Aligned: 113
Modelled: 113
Confidence: 100.0%
Identity: 52%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
4 |
| d1gd8a_ |

### PDB 1gd8 chain A

Region: 14 - 117
Aligned: 104
Modelled: 104
Confidence: 100.0%
Identity: 53%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
5 |
| d2cqma1 |

### PDB 2cqm chain A domain 1

Region: 20 - 124
Aligned: 105
Modelled: 105
Confidence: 100.0%
Identity: 34%
Fold: Prokaryotic ribosomal protein L17
Superfamily: Prokaryotic ribosomal protein L17
Family: Prokaryotic ribosomal protein L17

Phyre2
6 |
| c3h0dB_ |

### PDB 3h0d chain B

Region: 92 - 103
Aligned: 12
Modelled: 12
Confidence: 19.3%
Identity: 50%
PDB header:transcription/dna
Chain: B: PDB Molecule:ctsr;
PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex

Phyre2
7 |
| d1xd7a_ |

### PDB 1xd7 chain A

Region: 51 - 94
Aligned: 44
Modelled: 44
Confidence: 15.4%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Transcriptional regulator Rrf2

Phyre2
8 |
| d1o65a_ |

### PDB 1o65 chain A

Region: 89 - 125
Aligned: 32
Modelled: 37
Confidence: 15.0%
Identity: 25%
Fold: PK beta-barrel domain-like
Superfamily: PK beta-barrel domain-like
Family: MOSC (MOCO sulphurase C-terminal) domain

Phyre2
9 |
| c2op8A_ |

### PDB 2op8 chain A

Region: 11 - 31
Aligned: 21
Modelled: 21
Confidence: 14.1%
Identity: 5%
PDB header:isomerase
Chain: A: PDB Molecule:probable tautomerase ywhb;
PDBTitle: crystal structure of ywhb- homologue of 4-oxalocrotonate tautomerase

Phyre2
10 |
| c2z99A_ |

### PDB 2z99 chain A

Region: 42 - 95
Aligned: 53
Modelled: 54
Confidence: 13.5%
Identity: 26%
PDB header:cell cycle
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of scpb from mycobacterium tuberculosis

Phyre2
11 |
| c2ic6B_ |

### PDB 2ic6 chain B

Region: 33 - 84
Aligned: 52
Modelled: 52
Confidence: 13.3%
Identity: 23%
PDB header:viral protein
Chain: B: PDB Molecule:nucleocapsid protein;
PDBTitle: the coiled-coil domain (residues 1-75) structure of the sin2 nombre virus nucleocapsid protein

Phyre2
12 |
| c1x4qA_ |

### PDB 1x4q chain A

Region: 43 - 85
Aligned: 43
Modelled: 43
Confidence: 10.9%
Identity: 26%
PDB header:rna binding protein
Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3;
PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3)

Phyre2
13 |
| d1v66a_ |

### PDB 1v66 chain A

Region: 10 - 44
Aligned: 35
Modelled: 35
Confidence: 10.8%
Identity: 26%
Fold: LEM/SAP HeH motif
Superfamily: SAP domain
Family: SAP domain

Phyre2
14 |
| d1otfa_ |

### PDB 1otf chain A

Region: 11 - 31
Aligned: 21
Modelled: 21
Confidence: 9.9%
Identity: 10%
Fold: Tautomerase/MIF
Superfamily: Tautomerase/MIF
Family: 4-oxalocrotonate tautomerase-like

Phyre2
15 |
| d1bjpa_ |

### PDB 1bjp chain A

Region: 11 - 31
Aligned: 21
Modelled: 21
Confidence: 8.9%
Identity: 14%
Fold: Tautomerase/MIF
Superfamily: Tautomerase/MIF
Family: 4-oxalocrotonate tautomerase-like

Phyre2
16 |
| c3ry0A_ |

### PDB 3ry0 chain A

Region: 11 - 31
Aligned: 21
Modelled: 21
Confidence: 8.7%
Identity: 10%
PDB header:isomerase
Chain: A: PDB Molecule:putative tautomerase;
PDBTitle: crystal structure of tomn, a 4-oxalocrotonate tautomerase homologue in2 tomaymycin biosynthetic pathway

Phyre2
17 |
| c2qsgX_ |

### PDB 2qsg chain X

Region: 72 - 89
Aligned: 18
Modelled: 18
Confidence: 7.5%
Identity: 22%
PDB header:dna binding protein/dna
Chain: X: PDB Molecule:uv excision repair protein rad23;
PDBTitle: crystal structure of rad4-rad23 bound to a uv-damaged dna

Phyre2
18 |
| d2a7wa1 |

### PDB 2a7w chain A domain 1

Region: 74 - 95
Aligned: 22
Modelled: 22
Confidence: 7.2%
Identity: 14%
Fold: all-alpha NTP pyrophosphatases
Superfamily: all-alpha NTP pyrophosphatases
Family: HisE-like (PRA-PH)

Phyre2
19 |
| c2x4kB_ |

### PDB 2x4k chain B

Region: 11 - 30
Aligned: 20
Modelled: 20
Confidence: 6.8%
Identity: 5%
PDB header:isomerase
Chain: B: PDB Molecule:4-oxalocrotonate tautomerase;
PDBTitle: crystal structure of sar1376, a putative 4-oxalocrotonate2 tautomerase from the methicillin-resistant staphylococcus3 aureus (mrsa)

Phyre2
20 |
| c2a7wF_ |

### PDB 2a7w chain F

Region: 74 - 95
Aligned: 22
Modelled: 22
Confidence: 6.7%
Identity: 14%
PDB header:hydrolase
Chain: F: PDB Molecule:phosphoribosyl-atp pyrophosphatase;
PDBTitle: crystal structure of phosphoribosyl-atp pyrophosphatase2 from chromobacterium violaceum (atcc 12472). nesg target3 cvr7

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

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2qamn1 |
|  | 100.0 | 100 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
2 | c3bboP_ |
|  | 100.0 | 45 | 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
3 | d2zjrk1 |
|  | 100.0 | 52 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
4 | d1gd8a_ |
|  | 100.0 | 53 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
5 | d2cqma1 |
|  | 100.0 | 34 | Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17
6 | c3h0dB_ |
|  | 19.3 | 50 | PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex
7 | d1xd7a_ |
|  | 15.4 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator Rrf2
8 | d1o65a_ |
|  | 15.0 | 25 | Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:MOSC (MOCO sulphurase C-terminal) domain
9 | c2op8A_ |
|  | 14.1 | 5 | PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase ywhb; PDBTitle: crystal structure of ywhb- homologue of 4-oxalocrotonate tautomerase
10 | c2z99A_ |
|  | 13.5 | 26 | PDB header:cell cycle Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of scpb from mycobacterium tuberculosis
11 | c2ic6B_ |
|  | 13.3 | 23 | PDB header:viral protein Chain: B: PDB Molecule:nucleocapsid protein; PDBTitle: the coiled-coil domain (residues 1-75) structure of the sin2 nombre virus nucleocapsid protein
12 | c1x4qA_ |
|  | 10.9 | 26 | PDB header:rna binding protein Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3; PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3)
13 | d1v66a_ |
|  | 10.8 | 26 | Fold:LEM/SAP HeH motif Superfamily:SAP domain Family:SAP domain
14 | d1otfa_ |
|  | 9.9 | 10 | Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like
15 | d1bjpa_ |
|  | 8.9 | 14 | Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like
16 | c3ry0A_ |
|  | 8.7 | 10 | PDB header:isomerase Chain: A: PDB Molecule:putative tautomerase; PDBTitle: crystal structure of tomn, a 4-oxalocrotonate tautomerase homologue in2 tomaymycin biosynthetic pathway
17 | c2qsgX_ |
|  | 7.5 | 22 | PDB header:dna binding protein/dna Chain: X: PDB Molecule:uv excision repair protein rad23; PDBTitle: crystal structure of rad4-rad23 bound to a uv-damaged dna
18 | d2a7wa1 |
|  | 7.2 | 14 | Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH)
19 | c2x4kB_ |
|  | 6.8 | 5 | PDB header:isomerase Chain: B: PDB Molecule:4-oxalocrotonate tautomerase; PDBTitle: crystal structure of sar1376, a putative 4-oxalocrotonate2 tautomerase from the methicillin-resistant staphylococcus3 aureus (mrsa)
20 | c2a7wF_ |
|  | 6.7 | 14 | PDB header:hydrolase Chain: F: PDB Molecule:phosphoribosyl-atp pyrophosphatase; PDBTitle: crystal structure of phosphoribosyl-atp pyrophosphatase2 from chromobacterium violaceum (atcc 12472). nesg target3 cvr7
21 | d1x3zb1 |
| not modelled | 6.5 | 25 | Fold:XPC-binding domain Superfamily:XPC-binding domain Family:XPC-binding domain
22 | c2wb1J_ |
| not modelled | 6.2 | 19 | PDB header:transcription Chain: J: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase
23 | c3mb2G_ |
| not modelled | 6.1 | 10 | PDB header:isomerase Chain: G: PDB Molecule:4-oxalocrotonate tautomerase family enzyme - alpha subunit; PDBTitle: kinetic and structural characterization of a heterohexamer 4-2 oxalocrotonate tautomerase from chloroflexus aurantiacus j-10-fl:3 implications for functional and structural diversity in the4 tautomerase superfamily
24 | d2fufa1 |
| not modelled | 6.1 | 41 | Fold:Origin of replication-binding domain, RBD-like Superfamily:Origin of replication-binding domain, RBD-like Family:The origin DNA-binding domain of SV40 T-antigen
25 | c2p9xB_ |
| not modelled | 6.1 | 50 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3
26 | c2ormA_ |
| not modelled | 5.9 | 10 | PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase hp0924; PDBTitle: crystal structure of the 4-oxalocrotonate tautomerase homologue dmpi2 from helicobacter pylori.
27 | c3n4dF_ |
| not modelled | 5.7 | 5 | PDB header:hydrolase Chain: F: PDB Molecule:putative tautomerase; PDBTitle: crystal structure of cg10062 inactivated by(r)-oxirane-2-carboxylate
28 | d1y6xa1 |
| not modelled | 5.7 | 45 | Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH)
29 | d1mwwa_ |
| not modelled | 5.2 | 10 | Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:Hypothetical protein HI1388.1
30 | c3abfB_ |
| not modelled | 5.2 | 15 | PDB header:isomerase Chain: B: PDB Molecule:4-oxalocrotonate tautomerase; PDBTitle: crystal structure of a 4-oxalocrotonate tautomerase homologue2 (tthb242)

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