Phyre 2 Results for Q9Z3A0

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Email | l.a.kelley@imperial.ac.uk
Description | Q9Z3A0
Date | Thu Jan 5 12:38:31 GMT 2012
Unique Job ID | 1be3331859e83b7c

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3dw8B_
Top template information
PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:serine/threonine-protein phosphatase 2a 55 kda regulatory PDBTitle: structure of a protein phosphatase 2a holoenzyme with b55 subunit
Confidence and coverage
Confidence: | 22.0% | Coverage: | 35%
39 residues ( 35% of your sequence) have been modelled with 22.0% 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 | I | R | K | N | K | W | L | R | F | Q | T | V | C | R | Y | I | P | L | S | L | K | N | H | N | R | L | V | I | F | V | C | Q | R | I | E | W | R | Y | I | F | S | T | N | T | G | H | P | L | K | N | T | C | E | M | T | G | T | D | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | .
Sequence |  | S | T | D | G | L | M | R | R | Y | V | T | G | G | N | N | Q | W | H | T | V | A | S | L | H | M | T | I | M | M | N | R | I | G | T | V | A | D | R | Q | P | K | A | R | K | V | K | H | G | E | M | T
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 |
| c3dw8B_ |

### PDB 3dw8 chain B

Region: 35 - 75
Aligned: 39
Modelled: 41
Confidence: 22.0%
Identity: 15%
PDB header:hydrolase/hydrolase inhibitor
Chain: B: PDB Molecule:serine/threonine-protein phosphatase 2a 55 kda regulatory
PDBTitle: structure of a protein phosphatase 2a holoenzyme with b55 subunit

Phyre2
2 |
| d1jl3a_ |

### PDB 1jl3 chain A

Region: 25 - 32
Aligned: 8
Modelled: 8
Confidence: 18.7%
Identity: 38%
Fold: Phosphotyrosine protein phosphatases I-like
Superfamily: Phosphotyrosine protein phosphatases I
Family: Low-molecular-weight phosphotyrosine protein phosphatases

Phyre2
3 |
| c3nctC_ |

### PDB 3nct chain C

Region: 10 - 32
Aligned: 19
Modelled: 23
Confidence: 17.3%
Identity: 32%
PDB header:dna binding protein, chaperone
Chain: C: PDB Molecule:protein psib;
PDBTitle: x-ray crystal structure of the bacterial conjugation factor psib, a2 negative regulator of reca

Phyre2
4 |
| c2krcA_ |

### PDB 2krc chain A

Region: 58 - 77
Aligned: 17
Modelled: 20
Confidence: 16.2%
Identity: 35%
PDB header:transcription
Chain: A: PDB Molecule:dna-directed rna polymerase subunit delta;
PDBTitle: solution structure of the n-terminal domain of bacillus2 subtilis delta subunit of rna polymerase

Phyre2
5 |
| d2noca1 |

### PDB 2noc chain A domain 1

Region: 72 - 83
Aligned: 12
Modelled: 12
Confidence: 14.8%
Identity: 25%
Fold: Dodecin subunit-like
Superfamily: YdgH-like
Family: YdgH-like

Phyre2
6 |
| c2pxgA_ |

### PDB 2pxg chain A

Region: 37 - 67
Aligned: 31
Modelled: 31
Confidence: 9.2%
Identity: 13%
PDB header:membrane protein
Chain: A: PDB Molecule:outer membrane protein;
PDBTitle: nmr solution structure of omla

Phyre2
7 |
| c2jv5A_ |

### PDB 2jv5 chain A

Region: 43 - 51
Aligned: 9
Modelled: 9
Confidence: 8.5%
Identity: 33%
PDB header:protein binding
Chain: A: PDB Molecule:reticulon-4;
PDBTitle: nogo54

Phyre2
8 |
| c2kxxA_ |

### PDB 2kxx chain A

Region: 36 - 69
Aligned: 33
Modelled: 34
Confidence: 6.7%
Identity: 24%
PDB header:protein binding
Chain: A: PDB Molecule:small protein a;
PDBTitle: nmr structure of escherichia coli bame, a lipoprotein component of the2 beta-barrel assembly machinery complex

Phyre2
9 |
| d2igia1 |

### PDB 2igi chain A domain 1

Region: 53 - 67
Aligned: 15
Modelled: 15
Confidence: 6.6%
Identity: 40%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
10 |
| c1y8aA_ |

### PDB 1y8a chain A

Region: 38 - 57
Aligned: 20
Modelled: 20
Confidence: 6.5%
Identity: 30%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein af1437;
PDBTitle: structure of gene product af1437 from archaeoglobus fulgidus

Phyre2
11 |
| c2ko2A_ |

### PDB 2ko2 chain A

Region: 43 - 51
Aligned: 9
Modelled: 9
Confidence: 6.4%
Identity: 33%
PDB header:membrane protein
Chain: A: PDB Molecule:reticulon-4;
PDBTitle: nogo66

Phyre2
12 |
| c1x9dA_ |

### PDB 1x9d chain A

Region: 39 - 50
Aligned: 11
Modelled: 12
Confidence: 6.4%
Identity: 55%
PDB header:hydrolase
Chain: A: PDB Molecule:endoplasmic reticulum mannosyl-oligosaccharide 1,
PDBTitle: crystal structure of human class i alpha-1,2-mannosidase in2 complex with thio-disaccharide substrate analogue

Phyre2
13 |
| d1x9da1 |

### PDB 1x9d chain A domain 1

Region: 39 - 50
Aligned: 11
Modelled: 12
Confidence: 6.4%
Identity: 55%
Fold: alpha/alpha toroid
Superfamily: Seven-hairpin glycosidases
Family: Class I alpha-1;2-mannosidase, catalytic domain

Phyre2
14 |
| c2kerA_ |

### PDB 2ker chain A

Region: 37 - 44
Aligned: 8
Modelled: 8
Confidence: 6.0%
Identity: 50%
PDB header:hydrolase inhibitor
Chain: A: PDB Molecule:alpha-amylase inhibitor z-2685;
PDBTitle: alpha-amylase inhibitor parvulustat (z-2685) from2 streptomyces parvulus

Phyre2
15 |
| d1ok0a_ |

### PDB 1ok0 chain A

Region: 37 - 44
Aligned: 8
Modelled: 8
Confidence: 5.9%
Identity: 50%
Fold: alpha-Amylase inhibitor tendamistat
Superfamily: alpha-Amylase inhibitor tendamistat
Family: alpha-Amylase inhibitor tendamistat

Phyre2
16 |
| c3asiA_ |

### PDB 3asi chain A

Region: 74 - 81
Aligned: 8
Modelled: 8
Confidence: 5.8%
Identity: 63%
PDB header:cell adhesion
Chain: A: PDB Molecule:neurexin-1-alpha;
PDBTitle: alpha-neurexin-1 ectodomain fragment; lns5-egf3-lns6

Phyre2
17 |
| d1hcua_ |

### PDB 1hcu chain A

Region: 38 - 50
Aligned: 12
Modelled: 13
Confidence: 5.5%
Identity: 33%
Fold: alpha/alpha toroid
Superfamily: Seven-hairpin glycosidases
Family: Class I alpha-1;2-mannosidase, catalytic domain

Phyre2
18 |
| c3d3rA_ |

### PDB 3d3r chain A

Region: 8 - 18
Aligned: 11
Modelled: 11
Confidence: 5.5%
Identity: 55%
PDB header:chaperone
Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf;
PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1

Phyre2
19 |
| d1p2za2 |

### PDB 1p2z chain A domain 2

Region: 30 - 44
Aligned: 15
Modelled: 15
Confidence: 5.2%
Identity: 53%
Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily: Group II dsDNA viruses VP
Family: Adenovirus hexon

Phyre2
20 |
| d1hnfa2 |

### PDB 1hnf chain A domain 2

Region: 52 - 60
Aligned: 9
Modelled: 9
Confidence: 5.2%
Identity: 78%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: Immunoglobulin
Family: C2 set domains

Phyre2
21 |
22 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3dw8B_ |
|  | 22.0 | 15 | PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:serine/threonine-protein phosphatase 2a 55 kda regulatory PDBTitle: structure of a protein phosphatase 2a holoenzyme with b55 subunit
2 | d1jl3a_ |
|  | 18.7 | 38 | Fold:Phosphotyrosine protein phosphatases I-like Superfamily:Phosphotyrosine protein phosphatases I Family:Low-molecular-weight phosphotyrosine protein phosphatases
3 | c3nctC_ |
|  | 17.3 | 32 | PDB header:dna binding protein, chaperone Chain: C: PDB Molecule:protein psib; PDBTitle: x-ray crystal structure of the bacterial conjugation factor psib, a2 negative regulator of reca
4 | c2krcA_ |
|  | 16.2 | 35 | PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase subunit delta; PDBTitle: solution structure of the n-terminal domain of bacillus2 subtilis delta subunit of rna polymerase
5 | d2noca1 |
|  | 14.8 | 25 | Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like
6 | c2pxgA_ |
|  | 9.2 | 13 | PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein; PDBTitle: nmr solution structure of omla
7 | c2jv5A_ |
|  | 8.5 | 33 | PDB header:protein binding Chain: A: PDB Molecule:reticulon-4; PDBTitle: nogo54
8 | c2kxxA_ |
|  | 6.7 | 24 | PDB header:protein binding Chain: A: PDB Molecule:small protein a; PDBTitle: nmr structure of escherichia coli bame, a lipoprotein component of the2 beta-barrel assembly machinery complex
9 | d2igia1 |
|  | 6.6 | 40 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
10 | c1y8aA_ |
|  | 6.5 | 30 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein af1437; PDBTitle: structure of gene product af1437 from archaeoglobus fulgidus
11 | c2ko2A_ |
|  | 6.4 | 33 | PDB header:membrane protein Chain: A: PDB Molecule:reticulon-4; PDBTitle: nogo66
12 | c1x9dA_ |
|  | 6.4 | 55 | PDB header:hydrolase Chain: A: PDB Molecule:endoplasmic reticulum mannosyl-oligosaccharide 1, PDBTitle: crystal structure of human class i alpha-1,2-mannosidase in2 complex with thio-disaccharide substrate analogue
13 | d1x9da1 |
|  | 6.4 | 55 | Fold:alpha/alpha toroid Superfamily:Seven-hairpin glycosidases Family:Class I alpha-1;2-mannosidase, catalytic domain
14 | c2kerA_ |
|  | 6.0 | 50 | PDB header:hydrolase inhibitor Chain: A: PDB Molecule:alpha-amylase inhibitor z-2685; PDBTitle: alpha-amylase inhibitor parvulustat (z-2685) from2 streptomyces parvulus
15 | d1ok0a_ |
|  | 5.9 | 50 | Fold:alpha-Amylase inhibitor tendamistat Superfamily:alpha-Amylase inhibitor tendamistat Family:alpha-Amylase inhibitor tendamistat
16 | c3asiA_ |
|  | 5.8 | 63 | PDB header:cell adhesion Chain: A: PDB Molecule:neurexin-1-alpha; PDBTitle: alpha-neurexin-1 ectodomain fragment; lns5-egf3-lns6
17 | d1hcua_ |
|  | 5.5 | 33 | Fold:alpha/alpha toroid Superfamily:Seven-hairpin glycosidases Family:Class I alpha-1;2-mannosidase, catalytic domain
18 | c3d3rA_ |
|  | 5.5 | 55 | PDB header:chaperone Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf; PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1
19 | d1p2za2 |
|  | 5.2 | 53 | Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Adenovirus hexon
20 | d1hnfa2 |
|  | 5.2 | 78 | Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C2 set domains
21 | d2b5ib1 |
| not modelled | 5.1 | 36 | Fold:Immunoglobulin-like beta-sandwich Superfamily:Fibronectin type III Family:Fibronectin type III
22 | c3cxjB_ |
| not modelled | 5.0 | 32 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 methanothermobacter thermautotrophicus

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