Phyre 2 Results for P76001

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Email | l.a.kelley@imperial.ac.uk
Description | P76001
Date | Wed Jan 25 15:21:05 GMT 2012
Unique Job ID | 5b22f41c30a74fff

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1ig4a_
Top template information
Fold:DNA-binding domain Superfamily:DNA-binding domain Family:Methyl-CpG-binding domain, MBD
Confidence and coverage
Confidence: | 50.9% | Coverage: | 25%
31 residues ( 25% of your sequence) have been modelled with 50.9% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | N | M | M | R | I | F | Y | I | G | L | S | G | V | G | M | M | F | S | S | M | A | S | G | N | D | A | G | G | L | Q | S | P | A | C | G | V | V | C | D | P | Y | I | C | V | N | S | D | G | I | S | P | E | L | T | R | K | Y | L | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | E | K | A | A | E | N | L | Q | S | L | Q | G | Y | D | P | S | E | F | T | F | A | N | G | V | F | C | D | V | K | E | K | L | C | R | D | D | R | Y | F | G | V | D | G | K | R | S | G | K | I | N | Q | T | T | T | K | M | L | F | M | C
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | .
Sequence |  | R | 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 |
| d1ig4a_ |

### PDB 1ig4 chain A

Region: 51 - 91
Aligned: 31
Modelled: 41
Confidence: 50.9%
Identity: 32%
Fold: DNA-binding domain
Superfamily: DNA-binding domain
Family: Methyl-CpG-binding domain, MBD

Phyre2
2 |
| c2a2bA_ |

### PDB 2a2b chain A

Region: 79 - 97
Aligned: 17
Modelled: 19
Confidence: 49.6%
Identity: 41%
PDB header:antibiotic
Chain: A: PDB Molecule:bacteriocin curvacin a;
PDBTitle: curvacin a

Phyre2
3 |
| c2q3eH_ |

### PDB 2q3e chain H

Region: 1 - 21
Aligned: 21
Modelled: 21
Confidence: 16.6%
Identity: 29%
PDB header:oxidoreductase
Chain: H: PDB Molecule:udp-glucose 6-dehydrogenase;
PDBTitle: structure of human udp-glucose dehydrogenase complexed with nadh and2 udp-glucose

Phyre2
4 |
| d1flca1 |

### PDB 1flc chain A domain 1

Region: 39 - 49
Aligned: 11
Modelled: 11
Confidence: 11.7%
Identity: 45%
Fold: Viral protein domain
Superfamily: Viral protein domain
Family: Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1

Phyre2
5 |
| d1ua7a1 |

### PDB 1ua7 chain A domain 1

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 11.0%
Identity: 10%
Fold: Glycosyl hydrolase domain
Superfamily: Glycosyl hydrolase domain
Family: alpha-Amylases, C-terminal beta-sheet domain

Phyre2
6 |
| c3ebkA_ |

### PDB 3ebk chain A

Region: 78 - 113
Aligned: 32
Modelled: 36
Confidence: 9.9%
Identity: 22%
PDB header:allergen
Chain: A: PDB Molecule:allergen bla g 4;
PDBTitle: crystal structure of major allergens, bla g 4 from2 cockroaches

Phyre2
7 |
| c2yqpA_ |

### PDB 2yqp chain A

Region: 27 - 44
Aligned: 18
Modelled: 18
Confidence: 8.5%
Identity: 44%
PDB header:gene regulation, hydrolase
Chain: A: PDB Molecule:probable atp-dependent rna helicase ddx59;
PDBTitle: solution structure of the zf-hit domain in dead (asp-glu-2 ala-asp) box polypeptide 59

Phyre2
8 |
| d1q90r_ |

### PDB 1q90 chain R

Region: 1 - 24
Aligned: 24
Modelled: 24
Confidence: 8.5%
Identity: 33%
Fold: Single transmembrane helix
Superfamily: ISP transmembrane anchor
Family: ISP transmembrane anchor

Phyre2
9 |
| c1q90R_ |

### PDB 1q90 chain R

Region: 1 - 24
Aligned: 24
Modelled: 24
Confidence: 8.5%
Identity: 33%
PDB header:photosynthesis
Chain: R: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit;
PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii

Phyre2
10 |
| c3plnA_ |

### PDB 3pln chain A

Region: 2 - 21
Aligned: 20
Modelled: 20
Confidence: 8.1%
Identity: 25%
PDB header:oxidoreductase
Chain: A: PDB Molecule:udp-glucose 6-dehydrogenase;
PDBTitle: crystal structure of klebsiella pneumoniae udp-glucose 6-dehydrogenase2 complexed with udp-glucose

Phyre2
11 |
| d1qkia2 |

### PDB 1qki chain A domain 2

Region: 58 - 85
Aligned: 20
Modelled: 28
Confidence: 7.6%
Identity: 45%
Fold: FwdE/GAPDH domain-like
Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family: Glucose 6-phosphate dehydrogenase-like

Phyre2
12 |
| c3ggpA_ |

### PDB 3ggp chain A

Region: 1 - 41
Aligned: 36
Modelled: 38
Confidence: 7.5%
Identity: 19%
PDB header:oxidoreductase
Chain: A: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from a. aeolicus in2 complex with hydroxyphenyl propionate and nad+

Phyre2
13 |
| d1hx0a1 |

### PDB 1hx0 chain A domain 1

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 7.1%
Identity: 40%
Fold: Glycosyl hydrolase domain
Superfamily: Glycosyl hydrolase domain
Family: alpha-Amylases, C-terminal beta-sheet domain

Phyre2
14 |
| c3prjB_ |

### PDB 3prj chain B

Region: 1 - 21
Aligned: 21
Modelled: 21
Confidence: 7.0%
Identity: 29%
PDB header:oxidoreductase
Chain: B: PDB Molecule:udp-glucose 6-dehydrogenase;
PDBTitle: role of packing defects in the evolution of allostery and induced fit2 in human udp-glucose dehydrogenase.

Phyre2
15 |
| d1g94a1 |

### PDB 1g94 chain A domain 1

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 6.6%
Identity: 40%
Fold: Glycosyl hydrolase domain
Superfamily: Glycosyl hydrolase domain
Family: alpha-Amylases, C-terminal beta-sheet domain

Phyre2
16 |
| d1jaea1 |

### PDB 1jae chain A domain 1

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 6.6%
Identity: 40%
Fold: Glycosyl hydrolase domain
Superfamily: Glycosyl hydrolase domain
Family: alpha-Amylases, C-terminal beta-sheet domain

Phyre2
17 |
| c2bhlB_ |

### PDB 2bhl chain B

Region: 58 - 85
Aligned: 20
Modelled: 28
Confidence: 6.6%
Identity: 45%
PDB header:oxidoreductase (choh(d)-nadp)
Chain: B: PDB Molecule:glucose-6-phosphate 1-dehydrogenase;
PDBTitle: x-ray structure of human glucose-6-phosphate dehydrogenase2 (deletion variant) complexed with glucose-6-phosphate

Phyre2
18 |
| c1e0fI_ |

### PDB 1e0f chain I

Region: 83 - 110
Aligned: 27
Modelled: 28
Confidence: 6.5%
Identity: 37%
PDB header:coagulation/crystal structure/heparin-b
Chain: I: PDB Molecule:haemadin;
PDBTitle: crystal structure of the human alpha-thrombin-haemadin2 complex: an exosite ii-binding inhibitor

Phyre2
19 |
| d1e0fi_ |

### PDB 1e0f chain I

Region: 83 - 110
Aligned: 27
Modelled: 28
Confidence: 6.5%
Identity: 37%
Fold: Knottins (small inhibitors, toxins, lectins)
Superfamily: Leech antihemostatic proteins
Family: Hirudin-like

Phyre2
20 |
| d3dhpa1 |

### PDB 3dhp chain A domain 1

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 6.3%
Identity: 40%
Fold: Glycosyl hydrolase domain
Superfamily: Glycosyl hydrolase domain
Family: alpha-Amylases, C-terminal beta-sheet domain

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

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1ig4a_ |
|  | 50.9 | 32 | Fold:DNA-binding domain Superfamily:DNA-binding domain Family:Methyl-CpG-binding domain, MBD
2 | c2a2bA_ |
|  | 49.6 | 41 | PDB header:antibiotic Chain: A: PDB Molecule:bacteriocin curvacin a; PDBTitle: curvacin a
3 | c2q3eH_ |
|  | 16.6 | 29 | PDB header:oxidoreductase Chain: H: PDB Molecule:udp-glucose 6-dehydrogenase; PDBTitle: structure of human udp-glucose dehydrogenase complexed with nadh and2 udp-glucose
4 | d1flca1 |
|  | 11.7 | 45 | Fold:Viral protein domain Superfamily:Viral protein domain Family:Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1
5 | d1ua7a1 |
|  | 11.0 | 10 | Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain
6 | c3ebkA_ |
|  | 9.9 | 22 | PDB header:allergen Chain: A: PDB Molecule:allergen bla g 4; PDBTitle: crystal structure of major allergens, bla g 4 from2 cockroaches
7 | c2yqpA_ |
|  | 8.5 | 44 | PDB header:gene regulation, hydrolase Chain: A: PDB Molecule:probable atp-dependent rna helicase ddx59; PDBTitle: solution structure of the zf-hit domain in dead (asp-glu-2 ala-asp) box polypeptide 59
8 | d1q90r_ |
|  | 8.5 | 33 | Fold:Single transmembrane helix Superfamily:ISP transmembrane anchor Family:ISP transmembrane anchor
9 | c1q90R_ |
|  | 8.5 | 33 | PDB header:photosynthesis Chain: R: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii
10 | c3plnA_ |
|  | 8.1 | 25 | PDB header:oxidoreductase Chain: A: PDB Molecule:udp-glucose 6-dehydrogenase; PDBTitle: crystal structure of klebsiella pneumoniae udp-glucose 6-dehydrogenase2 complexed with udp-glucose
11 | d1qkia2 |
|  | 7.6 | 45 | Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Glucose 6-phosphate dehydrogenase-like
12 | c3ggpA_ |
|  | 7.5 | 19 | PDB header:oxidoreductase Chain: A: PDB Molecule:prephenate dehydrogenase; PDBTitle: crystal structure of prephenate dehydrogenase from a. aeolicus in2 complex with hydroxyphenyl propionate and nad+
13 | d1hx0a1 |
|  | 7.1 | 40 | Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain
14 | c3prjB_ |
|  | 7.0 | 29 | PDB header:oxidoreductase Chain: B: PDB Molecule:udp-glucose 6-dehydrogenase; PDBTitle: role of packing defects in the evolution of allostery and induced fit2 in human udp-glucose dehydrogenase.
15 | d1g94a1 |
|  | 6.6 | 40 | Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain
16 | d1jaea1 |
|  | 6.6 | 40 | Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain
17 | c2bhlB_ |
|  | 6.6 | 45 | PDB header:oxidoreductase (choh(d)-nadp) Chain: B: PDB Molecule:glucose-6-phosphate 1-dehydrogenase; PDBTitle: x-ray structure of human glucose-6-phosphate dehydrogenase2 (deletion variant) complexed with glucose-6-phosphate
18 | c1e0fI_ |
|  | 6.5 | 37 | PDB header:coagulation/crystal structure/heparin-b Chain: I: PDB Molecule:haemadin; PDBTitle: crystal structure of the human alpha-thrombin-haemadin2 complex: an exosite ii-binding inhibitor
19 | d1e0fi_ |
|  | 6.5 | 37 | Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Leech antihemostatic proteins Family:Hirudin-like
20 | d3dhpa1 |
|  | 6.3 | 40 | Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain
21 | d1t27a_ |
| not modelled | 6.2 | 16 | Fold:TBP-like Superfamily:Bet v1-like Family:Phoshatidylinositol transfer protein, PITP
22 | d1r0va3 |
| not modelled | 6.1 | 29 | Fold:MutS N-terminal domain-like Superfamily:tRNA-intron endonuclease N-terminal domain-like Family:tRNA-intron endonuclease N-terminal domain-like
23 | d1rmka_ |
| not modelled | 6.0 | 45 | Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Conotoxin
24 | d1h9aa1 |
| not modelled | 6.0 | 33 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
25 | c2l3bA_ |
| not modelled | 5.9 | 29 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein found in conjugate transposon; PDBTitle: solution nmr structure of the bt_0084 lipoprotein from bacteroides2 thetaiotaomicron, northeast structural genomics consortium target3 btr376
26 | d2a1la1 |
| not modelled | 5.9 | 20 | Fold:TBP-like Superfamily:Bet v1-like Family:Phoshatidylinositol transfer protein, PITP
27 | c2l7qA_ |
| not modelled | 5.9 | 33 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein found in conjugate transposon; PDBTitle: solution nmr structure of conjugate transposon protein bvu_1572(27-2 141) from bacteroides vulgatus, northeast structural genomics3 consortium target bvr155
28 | c1e0fJ_ |
| not modelled | 5.8 | 37 | PDB header:coagulation/crystal structure/heparin-b Chain: J: PDB Molecule:haemadin; PDBTitle: crystal structure of the human alpha-thrombin-haemadin2 complex: an exosite ii-binding inhibitor
29 | c1qkiE_ |
| not modelled | 5.5 | 45 | PDB header:oxidoreductase Chain: E: PDB Molecule:glucose-6-phosphate 1-dehydrogenase; PDBTitle: x-ray structure of human glucose 6-phosphate dehydrogenase2 (variant canton r459l) complexed with structural nadp+

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