Phyre 2 Results for P68919

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Email | l.a.kelley@imperial.ac.uk
Description | P68919
Date | Thu Jan 5 12:11:13 GMT 2012
Unique Job ID | 1fd58fc39f756b8e

Summary |

Top model
Image coloured by rainbow N → C terminus
| Close Jmol

Model (left) based on template d1dfup_
Top template information
Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Ribosomal protein L25-like
Confidence and coverage
Confidence: | 100.0% | Coverage: | 100%
94 residues (100% 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 | F | T | I | N | A | E | V | R | K | E | Q | G | K | G | A | S | R | R | L | R | A | A | N | K | F | P | A | I | I | Y | G | G | K | E | A | P | L | A | I | E | L | D | H | D | K | V | M | N | M | Q | A | K | A | E | F | Y | S | E | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | .
Sequence |  | L | T | I | V | V | D | G | K | E | I | K | V | K | A | Q | D | V | Q | R | H | P | Y | K | P | K | L | Q | H | I | D | F | V | R | A
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 |
| d1dfup_ |

### PDB 1dfu chain P

Region: 1 - 94
Aligned: 94
Modelled: 94
Confidence: 100.0%
Identity: 100%
Fold: Ribosomal protein L25-like
Superfamily: Ribosomal protein L25-like
Family: Ribosomal protein L25-like

Phyre2
2 |
| d1feua_ |

### PDB 1feu chain A

Region: 2 - 93
Aligned: 87
Modelled: 92
Confidence: 100.0%
Identity: 18%
Fold: Ribosomal protein L25-like
Superfamily: Ribosomal protein L25-like
Family: Ribosomal protein L25-like

Phyre2
3 |
| d2zjrs1 |

### PDB 2zjr chain S domain 1

Region: 2 - 93
Aligned: 84
Modelled: 92
Confidence: 99.9%
Identity: 19%
Fold: Ribosomal protein L25-like
Superfamily: Ribosomal protein L25-like
Family: Ribosomal protein L25-like

Phyre2
4 |
| c2b9nZ_ |

### PDB 2b9n chain Z

Region: 2 - 93
Aligned: 84
Modelled: 86
Confidence: 99.9%
Identity: 20%
PDB header:ribosome
Chain: Z: PDB Molecule:50s ribosomal protein ctc;
PDBTitle: 50s ribosomal subunit from a crystal structure of release factor rf2,2 trnas and mrna bound to the ribosome. this file contains the 50s3 subunit from a crystal structure of release factor rf1, trnas and4 mrna bound to the ribosome and is described in remark 400.

Phyre2
5 |
| d1zaka2 |

### PDB 1zak chain A domain 2

Region: 80 - 91
Aligned: 12
Modelled: 12
Confidence: 52.9%
Identity: 25%
Fold: Rubredoxin-like
Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
Family: Microbial and mitochondrial ADK, insert "zinc finger" domain

Phyre2
6 |
| d1htwa_ |

### PDB 1htw chain A

Region: 73 - 93
Aligned: 19
Modelled: 21
Confidence: 47.9%
Identity: 16%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: YjeE-like

Phyre2
7 |
| c1vhoA_ |

### PDB 1vho chain A

Region: 4 - 52
Aligned: 48
Modelled: 49
Confidence: 24.0%
Identity: 8%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:endoglucanase;
PDBTitle: crystal structure of a putative peptidase/endoglucanase

Phyre2
8 |
| c1q7lB_ |

### PDB 1q7l chain B

Region: 13 - 37
Aligned: 24
Modelled: 25
Confidence: 18.0%
Identity: 25%
PDB header:hydrolase
Chain: B: PDB Molecule:aminoacylase-1;
PDBTitle: zn-binding domain of the t347g mutant of human aminoacylase-2 i

Phyre2
9 |
| c3no8A_ |

### PDB 3no8 chain A

Region: 22 - 31
Aligned: 10
Modelled: 10
Confidence: 14.8%
Identity: 20%
PDB header:isomerase regulator
Chain: A: PDB Molecule:btb/poz domain-containing protein 2;
PDBTitle: crystal structure of the phr domain from human btbd2 protein

Phyre2
10 |
| c1vixA_ |

### PDB 1vix chain A

Region: 4 - 39
Aligned: 35
Modelled: 36
Confidence: 14.8%
Identity: 14%
PDB header:hydrolase
Chain: A: PDB Molecule:peptidase t;
PDBTitle: crystal structure of a putative peptidase t

Phyre2
11 |
| d2phpa1 |

### PDB 2php chain A domain 1

Region: 15 - 38
Aligned: 24
Modelled: 23
Confidence: 12.8%
Identity: 29%
Fold: AraD/HMP-PK domain-like
Superfamily: AraD/HMP-PK domain-like
Family: Phosphomethylpyrimidine kinase C-terminal domain-like

Phyre2
12 |
| d1a6ca3 |

### PDB 1a6c chain A domain 3

Region: 25 - 65
Aligned: 41
Modelled: 41
Confidence: 12.2%
Identity: 10%
Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily: Positive stranded ssRNA viruses
Family: Comoviridae-like VP

Phyre2
13 |
| c3hwjA_ |

### PDB 3hwj chain A

Region: 23 - 31
Aligned: 9
Modelled: 9
Confidence: 11.2%
Identity: 33%
PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase mycbp2;
PDBTitle: crystal structure of the second phr domain of mouse myc-2 binding protein 2 (mycbp-2)

Phyre2
14 |
| c3l7pA_ |

### PDB 3l7p chain A

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 11.0%
Identity: 17%
PDB header:transcription
Chain: A: PDB Molecule:putative nitrogen regulatory protein pii;
PDBTitle: crystal structure of smu.1657c, putative nitrogen regulatory protein2 pii from streptococcus mutans

Phyre2
15 |
| d1etha1 |

### PDB 1eth chain A domain 1

Region: 23 - 90
Aligned: 63
Modelled: 68
Confidence: 10.6%
Identity: 14%
Fold: Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily: Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family: Colipase-binding domain

Phyre2
16 |
| c3rzaA_ |

### PDB 3rza chain A

Region: 11 - 52
Aligned: 41
Modelled: 42
Confidence: 9.6%
Identity: 10%
PDB header:hydrolase
Chain: A: PDB Molecule:tripeptidase;
PDBTitle: crystal structure of a tripeptidase (sav1512) from staphylococcus2 aureus subsp. aureus mu50 at 2.10 a resolution

Phyre2
17 |
| c3na2C_ |

### PDB 3na2 chain C

Region: 28 - 82
Aligned: 55
Modelled: 55
Confidence: 9.5%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of protein of unknown function from mine drainage2 metagenome leptospirillum rubarum

Phyre2
18 |
| c3ls8A_ |

### PDB 3ls8 chain A

Region: 83 - 91
Aligned: 9
Modelled: 9
Confidence: 9.3%
Identity: 67%
PDB header:transferase
Chain: A: PDB Molecule:phosphatidylinositol 3-kinase catalytic subunit
PDBTitle: crystal structure of human pik3c3 in complex with 3-[4-(4-2 morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol

Phyre2
19 |
| d1z2la1 |

### PDB 1z2l chain A domain 1

Region: 4 - 34
Aligned: 30
Modelled: 31
Confidence: 9.3%
Identity: 10%
Fold: Phosphorylase/hydrolase-like
Superfamily: Zn-dependent exopeptidases
Family: Bacterial dinuclear zinc exopeptidases

Phyre2
20 |
| d1vjna_ |

### PDB 1vjn chain A

Region: 15 - 78
Aligned: 62
Modelled: 64
Confidence: 8.9%
Identity: 24%
Fold: Metallo-hydrolase/oxidoreductase
Superfamily: Metallo-hydrolase/oxidoreductase
Family: Hypothetical protein TM0207

Phyre2
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43 |
44 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1dfup_ |
|  | 100.0 | 100 | Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Ribosomal protein L25-like
2 | d1feua_ |
|  | 100.0 | 18 | Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Ribosomal protein L25-like
3 | d2zjrs1 |
|  | 99.9 | 19 | Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Ribosomal protein L25-like
4 | c2b9nZ_ |
|  | 99.9 | 20 | PDB header:ribosome Chain: Z: PDB Molecule:50s ribosomal protein ctc; PDBTitle: 50s ribosomal subunit from a crystal structure of release factor rf2,2 trnas and mrna bound to the ribosome. this file contains the 50s3 subunit from a crystal structure of release factor rf1, trnas and4 mrna bound to the ribosome and is described in remark 400.
5 | d1zaka2 |
|  | 52.9 | 25 | Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
6 | d1htwa_ |
|  | 47.9 | 16 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:YjeE-like
7 | c1vhoA_ |
|  | 24.0 | 8 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:endoglucanase; PDBTitle: crystal structure of a putative peptidase/endoglucanase
8 | c1q7lB_ |
|  | 18.0 | 25 | PDB header:hydrolase Chain: B: PDB Molecule:aminoacylase-1; PDBTitle: zn-binding domain of the t347g mutant of human aminoacylase-2 i
9 | c3no8A_ |
|  | 14.8 | 20 | PDB header:isomerase regulator Chain: A: PDB Molecule:btb/poz domain-containing protein 2; PDBTitle: crystal structure of the phr domain from human btbd2 protein
10 | c1vixA_ |
|  | 14.8 | 14 | PDB header:hydrolase Chain: A: PDB Molecule:peptidase t; PDBTitle: crystal structure of a putative peptidase t
11 | d2phpa1 |
|  | 12.8 | 29 | Fold:AraD/HMP-PK domain-like Superfamily:AraD/HMP-PK domain-like Family:Phosphomethylpyrimidine kinase C-terminal domain-like
12 | d1a6ca3 |
|  | 12.2 | 10 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP
13 | c3hwjA_ |
|  | 11.2 | 33 | PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase mycbp2; PDBTitle: crystal structure of the second phr domain of mouse myc-2 binding protein 2 (mycbp-2)
14 | c3l7pA_ |
|  | 11.0 | 17 | PDB header:transcription Chain: A: PDB Molecule:putative nitrogen regulatory protein pii; PDBTitle: crystal structure of smu.1657c, putative nitrogen regulatory protein2 pii from streptococcus mutans
15 | d1etha1 |
|  | 10.6 | 14 | Fold:Lipase/lipooxygenase domain (PLAT/LH2 domain) Superfamily:Lipase/lipooxygenase domain (PLAT/LH2 domain) Family:Colipase-binding domain
16 | c3rzaA_ |
|  | 9.6 | 10 | PDB header:hydrolase Chain: A: PDB Molecule:tripeptidase; PDBTitle: crystal structure of a tripeptidase (sav1512) from staphylococcus2 aureus subsp. aureus mu50 at 2.10 a resolution
17 | c3na2C_ |
|  | 9.5 | 18 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of protein of unknown function from mine drainage2 metagenome leptospirillum rubarum
18 | c3ls8A_ |
|  | 9.3 | 67 | PDB header:transferase Chain: A: PDB Molecule:phosphatidylinositol 3-kinase catalytic subunit PDBTitle: crystal structure of human pik3c3 in complex with 3-[4-(4-2 morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol
19 | d1z2la1 |
|  | 9.3 | 10 | Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases
20 | d1vjna_ |
|  | 8.9 | 24 | Fold:Metallo-hydrolase/oxidoreductase Superfamily:Metallo-hydrolase/oxidoreductase Family:Hypothetical protein TM0207
21 | c3gbwA_ |
| not modelled | 8.8 | 33 | PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase mycbp2; PDBTitle: crystal structure of the first phr domain of the mouse myc-2 binding protein 2 (mycbp-2)
22 | c2j8aA_ |
| not modelled | 8.6 | 14 | PDB header:transferase Chain: A: PDB Molecule:histone-lysine n-methyltransferase, h3 lysine-4 PDBTitle: x-ray structure of the n-terminus rrm domain of set1
23 | d1e7ua4 |
| not modelled | 8.3 | 56 | Fold:Protein kinase-like (PK-like) Superfamily:Protein kinase-like (PK-like) Family:Phoshoinositide 3-kinase (PI3K), catalytic domain
24 | c2x6kB_ |
| not modelled | 7.5 | 67 | PDB header:transferase Chain: B: PDB Molecule:phosphotidylinositol 3 kinase 59f; PDBTitle: the crystal structure of the drosophila class iii pi3-kinase2 vps34 in complex with pi-103
25 | c3ifeA_ |
| not modelled | 7.4 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:peptidase t; PDBTitle: 1.55 angstrom resolution crystal structure of peptidase t (pept-1)2 from bacillus anthracis str. 'ames ancestor'.
26 | d1qo5b_ |
| not modelled | 7.1 | 29 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
27 | c3mmtC_ |
| not modelled | 7.0 | 26 | PDB header:hydrolase Chain: C: PDB Molecule:fructose-bisphosphate aldolase; PDBTitle: crystal structure of fructose bisphosphate aldolase from bartonella2 henselae, bound to fructose bisphosphate
28 | d1fdja_ |
| not modelled | 6.6 | 29 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
29 | d1vixa1 |
| not modelled | 6.4 | 14 | Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases
30 | d1xfba1 |
| not modelled | 6.4 | 19 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
31 | d1vkia_ |
| not modelled | 6.3 | 5 | Fold:YbaK/ProRS associated domain Superfamily:YbaK/ProRS associated domain Family:YbaK/ProRS associated domain
32 | d1zaia1 |
| not modelled | 6.2 | 16 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
33 | c2x0oA_ |
| not modelled | 6.2 | 21 | PDB header:biosynthetic protein Chain: A: PDB Molecule:alcaligin biosynthesis protein; PDBTitle: apo structure of the alcaligin biosynthesis protein c (alcc)2 from bordetella bronchiseptica
34 | c2pc4B_ |
| not modelled | 6.0 | 19 | PDB header:lyase Chain: B: PDB Molecule:fructose-bisphosphate aldolase; PDBTitle: crystal structure of fructose-bisphosphate aldolase from plasmodium2 falciparum in complex with trap-tail determined at 2.4 angstrom3 resolution
35 | d1a5ca_ |
| not modelled | 5.7 | 19 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
36 | c2rb7A_ |
| not modelled | 5.7 | 19 | PDB header:hydrolase Chain: A: PDB Molecule:peptidase, m20/m25/m40 family; PDBTitle: crystal structure of co-catalytic metallopeptidase (yp_387682.1) from2 desulfovibrio desulfuricans g20 at 1.60 a resolution
37 | d1fbaa_ |
| not modelled | 5.7 | 16 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
38 | d1f2ja_ |
| not modelled | 5.4 | 23 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
39 | d1nn7a_ |
| not modelled | 5.3 | 17 | Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels
40 | c2y3aA_ |
| not modelled | 5.1 | 56 | PDB header:transferase Chain: A: PDB Molecule:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic PDBTitle: crystal structure of p110beta in complex with icsh2 of p85beta and2 the drug gdc-0941
41 | c3ic1A_ |
| not modelled | 5.1 | 9 | PDB header:hydrolase Chain: A: PDB Molecule:succinyl-diaminopimelate desuccinylase; PDBTitle: crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase2 from haemophilus influenzae
42 | d1s1ga_ |
| not modelled | 5.1 | 19 | Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels
43 | c1e8zA_ |
| not modelled | 5.0 | 56 | PDB header:transferase Chain: A: PDB Molecule:phosphatidylinositol 3-kinase catalytic subunit; PDBTitle: structure determinants of phosphoinositide 3-kinase2 inhibition by wortmannin, ly294002, quercetin, myricetin3 and staurosporine
44 | d2hgca1 |
| not modelled | 5.0 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:YjcQ-like

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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Terms and Conditions
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