Phyre 2 Results for P41070

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Email | l.a.kelley@imperial.ac.uk
Description | P41070
Date | Thu Jan 5 12:01:26 GMT 2012
Unique Job ID | 89f628c8618f3a09

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1e9ra_
Top template information
Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain)
Confidence and coverage
Confidence: | 50.1% | Coverage: | 58%
38 residues ( 58% of your sequence) have been modelled with 50.1% 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 | R | N | I | N | V | I | T | V | L | S | V | P | G | K | T | V | S | D | D | F | M | H | A | V | L | S | N | C | A | T | R | I | V | L | P | A | P | E | K | F | G | S | E | S | L | P | D | N | F | N | M | T | A | V | G | V | M
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | .
Sequence |  | K | N | S | E | I
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 |
| d1e9ra_ |

### PDB 1e9r chain A

Region: 3 - 40
Aligned: 38
Modelled: 38
Confidence: 50.1%
Identity: 11%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: RecA protein-like (ATPase-domain)

Phyre2
2 |
| d2pvaa_ |

### PDB 2pva chain A

Region: 20 - 33
Aligned: 14
Modelled: 14
Confidence: 12.9%
Identity: 36%
Fold: Ntn hydrolase-like
Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family: Penicillin V acylase

Phyre2
3 |
| c2hezB_ |

### PDB 2hez chain B

Region: 20 - 33
Aligned: 14
Modelled: 14
Confidence: 11.5%
Identity: 21%
PDB header:hydrolase
Chain: B: PDB Molecule:bile salt hydrolase;
PDBTitle: bifidobacterium longum bile salt hydrolase

Phyre2
4 |
| c1shzF_ |

### PDB 1shz chain F

Region: 23 - 30
Aligned: 8
Modelled: 8
Confidence: 10.4%
Identity: 13%
PDB header:signaling protein
Chain: F: PDB Molecule:rho guanine nucleotide exchange factor 1;
PDBTitle: crystal structure of the p115rhogef rgrgs domain in a2 complex with galpha(13):galpha(i1) chimera

Phyre2
5 |
| c2bjgB_ |

### PDB 2bjg chain B

Region: 20 - 33
Aligned: 14
Modelled: 14
Confidence: 10.3%
Identity: 29%
PDB header:hydrolase
Chain: B: PDB Molecule:choloylglycine hydrolase;
PDBTitle: crystal structure of conjugated bile acid hydrolase from2 clostridium perfringens in complex with reaction products3 taurine and deoxycholate

Phyre2
6 |
| d1iapa_ |

### PDB 1iap chain A

Region: 23 - 30
Aligned: 8
Modelled: 8
Confidence: 10.3%
Identity: 13%
Fold: Regulator of G-protein signaling, RGS
Superfamily: Regulator of G-protein signaling, RGS
Family: Regulator of G-protein signaling, RGS

Phyre2
7 |
| d1htjf_ |

### PDB 1htj chain F

Region: 23 - 30
Aligned: 8
Modelled: 8
Confidence: 9.2%
Identity: 25%
Fold: Regulator of G-protein signaling, RGS
Superfamily: Regulator of G-protein signaling, RGS
Family: Regulator of G-protein signaling, RGS

Phyre2
8 |
| c1htjF_ |

### PDB 1htj chain F

Region: 23 - 30
Aligned: 8
Modelled: 8
Confidence: 9.2%
Identity: 25%
PDB header:signaling protein
Chain: F: PDB Molecule:kiaa0380;
PDBTitle: structure of the rgs-like domain from pdz-rhogef

Phyre2
9 |
| d2jxta1 |

### PDB 2jxt chain A domain 1

Region: 4 - 28
Aligned: 25
Modelled: 25
Confidence: 9.0%
Identity: 12%
Fold: RplX-like
Superfamily: RplX-like
Family: RplX-like

Phyre2
10 |
| c1tu3J_ |

### PDB 1tu3 chain J

Region: 17 - 25
Aligned: 9
Modelled: 9
Confidence: 8.7%
Identity: 33%
PDB header:protein transport
Chain: J: PDB Molecule:rab gtpase binding effector protein 1;
PDBTitle: crystal structure of rab5 complex with rabaptin5 c-terminal2 domain

Phyre2
11 |
| c3aqbC_ |

### PDB 3aqb chain C

Region: 20 - 35
Aligned: 14
Modelled: 16
Confidence: 8.4%
Identity: 50%
PDB header:transferase
Chain: C: PDB Molecule:component a of hexaprenyl diphosphate synthase;
PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium

Phyre2
12 |
| d2f4ia1 |

### PDB 2f4i chain A domain 1

Region: 39 - 64
Aligned: 26
Modelled: 26
Confidence: 7.4%
Identity: 15%
Fold: OB-fold
Superfamily: TM0957-like
Family: TM0957-like

Phyre2
13 |
| c3ipjB_ |

### PDB 3ipj chain B

Region: 28 - 37
Aligned: 10
Modelled: 10
Confidence: 6.6%
Identity: 40%
PDB header:transferase
Chain: B: PDB Molecule:pts system, iiabc component;
PDBTitle: the crystal structure of one domain of the pts system, iiabc component2 from clostridium difficile

Phyre2
14 |
| c2oqcB_ |

### PDB 2oqc chain B

Region: 22 - 33
Aligned: 12
Modelled: 12
Confidence: 6.0%
Identity: 42%
PDB header:hydrolase
Chain: B: PDB Molecule:penicillin v acylase;
PDBTitle: crystal structure of penicillin v acylase from bacillus subtilis

Phyre2
15 |
| c1ibaA_ |

### PDB 1iba chain A

Region: 28 - 37
Aligned: 10
Modelled: 10
Confidence: 5.9%
Identity: 40%
PDB header:phoshphotransferase
Chain: A: PDB Molecule:glucose permease;
PDBTitle: glucose permease (domain iib), nmr, 11 structures

Phyre2
16 |
| c3hbcA_ |

### PDB 3hbc chain A

Region: 22 - 33
Aligned: 12
Modelled: 12
Confidence: 5.6%
Identity: 42%
PDB header:hydrolase
Chain: A: PDB Molecule:choloylglycine hydrolase;
PDBTitle: crystal structure of choloylglycine hydrolase from bacteroides2 thetaiotaomicron vpi

Phyre2
17 |
| d3bp8c1 |

### PDB 3bp8 chain C domain 1

Region: 28 - 37
Aligned: 10
Modelled: 10
Confidence: 5.2%
Identity: 40%
Fold: Homing endonuclease-like
Superfamily: Glucose permease domain IIB
Family: Glucose permease domain IIB

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1e9ra_ |
|  | 50.1 | 11 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain)
2 | d2pvaa_ |
|  | 12.9 | 36 | Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Penicillin V acylase
3 | c2hezB_ |
|  | 11.5 | 21 | PDB header:hydrolase Chain: B: PDB Molecule:bile salt hydrolase; PDBTitle: bifidobacterium longum bile salt hydrolase
4 | c1shzF_ |
|  | 10.4 | 13 | PDB header:signaling protein Chain: F: PDB Molecule:rho guanine nucleotide exchange factor 1; PDBTitle: crystal structure of the p115rhogef rgrgs domain in a2 complex with galpha(13):galpha(i1) chimera
5 | c2bjgB_ |
|  | 10.3 | 29 | PDB header:hydrolase Chain: B: PDB Molecule:choloylglycine hydrolase; PDBTitle: crystal structure of conjugated bile acid hydrolase from2 clostridium perfringens in complex with reaction products3 taurine and deoxycholate
6 | d1iapa_ |
|  | 10.3 | 13 | Fold:Regulator of G-protein signaling, RGS Superfamily:Regulator of G-protein signaling, RGS Family:Regulator of G-protein signaling, RGS
7 | d1htjf_ |
|  | 9.2 | 25 | Fold:Regulator of G-protein signaling, RGS Superfamily:Regulator of G-protein signaling, RGS Family:Regulator of G-protein signaling, RGS
8 | c1htjF_ |
|  | 9.2 | 25 | PDB header:signaling protein Chain: F: PDB Molecule:kiaa0380; PDBTitle: structure of the rgs-like domain from pdz-rhogef
9 | d2jxta1 |
|  | 9.0 | 12 | Fold:RplX-like Superfamily:RplX-like Family:RplX-like
10 | c1tu3J_ |
|  | 8.7 | 33 | PDB header:protein transport Chain: J: PDB Molecule:rab gtpase binding effector protein 1; PDBTitle: crystal structure of rab5 complex with rabaptin5 c-terminal2 domain
11 | c3aqbC_ |
|  | 8.4 | 50 | PDB header:transferase Chain: C: PDB Molecule:component a of hexaprenyl diphosphate synthase; PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium
12 | d2f4ia1 |
|  | 7.4 | 15 | Fold:OB-fold Superfamily:TM0957-like Family:TM0957-like
13 | c3ipjB_ |
|  | 6.6 | 40 | PDB header:transferase Chain: B: PDB Molecule:pts system, iiabc component; PDBTitle: the crystal structure of one domain of the pts system, iiabc component2 from clostridium difficile
14 | c2oqcB_ |
|  | 6.0 | 42 | PDB header:hydrolase Chain: B: PDB Molecule:penicillin v acylase; PDBTitle: crystal structure of penicillin v acylase from bacillus subtilis
15 | c1ibaA_ |
|  | 5.9 | 40 | PDB header:phoshphotransferase Chain: A: PDB Molecule:glucose permease; PDBTitle: glucose permease (domain iib), nmr, 11 structures
16 | c3hbcA_ |
|  | 5.6 | 42 | PDB header:hydrolase Chain: A: PDB Molecule:choloylglycine hydrolase; PDBTitle: crystal structure of choloylglycine hydrolase from bacteroides2 thetaiotaomicron vpi
17 | d3bp8c1 |
|  | 5.2 | 40 | Fold:Homing endonuclease-like Superfamily:Glucose permease domain IIB Family:Glucose permease domain IIB

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