Phyre 2 Results for P55914

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Email | l.a.kelley@imperial.ac.uk
Description | P55914
Date | Thu Jan 5 12:06:16 GMT 2012
Unique Job ID | 27d956e0fe053796

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2rddB_
Top template information
PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.
Confidence and coverage
Confidence: | 11.7% | Coverage: | 22%
17 residues ( 22% of your sequence) have been modelled with 11.7% confidence by the single highest scoring template.
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Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | L | Q | R | T | L | G | S | G | W | G | V | L | L | P | G | L | L | I | A | G | L | M | Y | A | D | L | S | S | D | Q | W | R | I | V | I | L | M | G | L | V | L | T | P | M | M | L | Y | H | K | Q | L | R | H | Y | I | L | L | P | S
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
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Sequence |  | C | L | A | L | I | A | G | I | M | L | M | I | M | N | L | N | Q | G
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 |
| c2rddB_ |

### PDB 2rdd chain B

Region: 8 - 24
Aligned: 17
Modelled: 17
Confidence: 11.7%
Identity: 18%
PDB header:membrane protein/transport protein
Chain: B: PDB Molecule:upf0092 membrane protein yajc;
PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.

Phyre2
2 |
| c2ostC_ |

### PDB 2ost chain C

Region: 4 - 15
Aligned: 12
Modelled: 12
Confidence: 10.6%
Identity: 67%
PDB header:hydrolase/dna
Chain: C: PDB Molecule:putative endonuclease;
PDBTitle: the structure of a bacterial homing endonuclease : i-ssp6803i

Phyre2
3 |
| d2al6a2 |

### PDB 2al6 chain A domain 2

Region: 5 - 12
Aligned: 8
Modelled: 8
Confidence: 8.7%
Identity: 50%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Third domain of FERM

Phyre2
4 |
| d1uerc2 |

### PDB 1uer chain C domain 2

Region: 7 - 14
Aligned: 8
Modelled: 8
Confidence: 8.7%
Identity: 63%
Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain

Phyre2
5 |
| c2bf9A_ |

### PDB 2bf9 chain A

Region: 48 - 58
Aligned: 11
Modelled: 11
Confidence: 8.6%
Identity: 18%
PDB header:hormone
Chain: A: PDB Molecule:pancreatic hormone;
PDBTitle: anisotropic refinement of avian (turkey) pancreatic2 polypeptide at 0.99 angstroms resolution.

Phyre2
6 |
| c2nr1A_ |

### PDB 2nr1 chain A

Region: 10 - 14
Aligned: 5
Modelled: 5
Confidence: 7.7%
Identity: 100%
PDB header:receptor
Chain: A: PDB Molecule:nr1 m2;
PDBTitle: transmembrane segment 2 of nmda receptor nr1, nmr, 102 structures

Phyre2
7 |
| c3gycB_ |

### PDB 3gyc chain B

Region: 48 - 57
Aligned: 10
Modelled: 10
Confidence: 7.5%
Identity: 40%
PDB header:hydrolase
Chain: B: PDB Molecule:putative glycoside hydrolase;
PDBTitle: crystal structure of putative glycoside hydrolase (yp_001304622.1)2 from parabacteroides distasonis atcc 8503 at 1.85 a resolution

Phyre2
8 |
| c1wqsA_ |

### PDB 1wqs chain A

Region: 5 - 11
Aligned: 7
Modelled: 7
Confidence: 7.1%
Identity: 71%
PDB header:hydrolase
Chain: A: PDB Molecule:3c-like protease;
PDBTitle: crystal structure of norovirus 3c-like protease

Phyre2
9 |
| c3h1sB_ |

### PDB 3h1s chain B

Region: 7 - 14
Aligned: 8
Modelled: 8
Confidence: 6.9%
Identity: 63%
PDB header:oxidoreductase
Chain: B: PDB Molecule:superoxide dismutase;
PDBTitle: crystal structure of superoxide dismutase from francisella tularensis2 subsp. tularensis schu s4

Phyre2
10 |
| c2dezA_ |

### PDB 2dez chain A

Region: 48 - 58
Aligned: 11
Modelled: 11
Confidence: 6.6%
Identity: 55%
PDB header:neuropeptide
Chain: A: PDB Molecule:peptide yy;
PDBTitle: structure of human pyy

Phyre2
11 |
| c1dt0A_ |

### PDB 1dt0 chain A

Region: 7 - 14
Aligned: 8
Modelled: 8
Confidence: 6.6%
Identity: 75%
PDB header:oxidoreductase
Chain: A: PDB Molecule:superoxide dismutase;
PDBTitle: cloning, sequence, and crystallographic structure of2 recombinant iron superoxide dismutase from pseudomonas3 ovalis

Phyre2
12 |
| c1ronA_ |

### PDB 1ron chain A

Region: 48 - 58
Aligned: 11
Modelled: 11
Confidence: 6.6%
Identity: 64%
PDB header:neuropeptide
Chain: A: PDB Molecule:neuropeptide y;
PDBTitle: nmr solution structure of human neuropeptide y

Phyre2
13 |
| c2vdaB_ |

### PDB 2vda chain B

Region: 58 - 69
Aligned: 12
Modelled: 12
Confidence: 6.4%
Identity: 50%
PDB header:protein transport
Chain: B: PDB Molecule:maltoporin;
PDBTitle: solution structure of the seca-signal peptide complex

Phyre2
14 |
| d2z0da1 |

### PDB 2z0d chain A domain 1

Region: 5 - 14
Aligned: 10
Modelled: 10
Confidence: 6.2%
Identity: 50%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Autophagin-like

Phyre2
15 |
| c2hv8D_ |

### PDB 2hv8 chain D

Region: 50 - 56
Aligned: 7
Modelled: 7
Confidence: 6.2%
Identity: 43%
PDB header:protein transport
Chain: D: PDB Molecule:rab11 family-interacting protein 3;
PDBTitle: crystal structure of gtp-bound rab11 in complex with fip3

Phyre2
16 |
| c1tz5A_ |

### PDB 1tz5 chain A

Region: 48 - 58
Aligned: 11
Modelled: 11
Confidence: 6.1%
Identity: 45%
PDB header:hormone/growth factor
Chain: A: PDB Molecule:chimera of pancreatic hormone and neuropeptide y;
PDBTitle: [pnpy19-23]-hpp bound to dpc micelles

Phyre2
17 |
| d1kkca2 |

### PDB 1kkc chain A domain 2

Region: 7 - 14
Aligned: 8
Modelled: 8
Confidence: 5.7%
Identity: 75%
Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain

Phyre2
18 |
| d2j01p1 |

### PDB 2j01 chain P domain 1

Region: 4 - 11
Aligned: 8
Modelled: 8
Confidence: 5.5%
Identity: 63%
Fold: Ribosomal proteins L15p and L18e
Superfamily: Ribosomal proteins L15p and L18e
Family: Ribosomal proteins L15p and L18e

Phyre2
19 |
| c1qnnD_ |

### PDB 1qnn chain D

Region: 7 - 14
Aligned: 8
Modelled: 8
Confidence: 5.5%
Identity: 63%
PDB header:oxidoreductase
Chain: D: PDB Molecule:superoxide dismutase;
PDBTitle: cambialistic superoxide dismutase from porphyromonas2 gingivalis

Phyre2
20 |
| c1my6A_ |

### PDB 1my6 chain A

Region: 7 - 14
Aligned: 8
Modelled: 8
Confidence: 5.4%
Identity: 63%
PDB header:oxidoreductase
Chain: A: PDB Molecule:iron (iii) superoxide dismutase;
PDBTitle: the 1.6 a structure of fe-superoxide dismutase from the2 thermophilic cyanobacterium thermosynechococcus elongatus3 : correlation of epr and structural characteristics

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

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2rddB_ |
|  | 11.7 | 18 | PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.
2 | c2ostC_ |
|  | 10.6 | 67 | PDB header:hydrolase/dna Chain: C: PDB Molecule:putative endonuclease; PDBTitle: the structure of a bacterial homing endonuclease : i-ssp6803i
3 | d2al6a2 |
|  | 8.7 | 50 | Fold:PH domain-like barrel Superfamily:PH domain-like Family:Third domain of FERM
4 | d1uerc2 |
|  | 8.7 | 63 | Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain
5 | c2bf9A_ |
|  | 8.6 | 18 | PDB header:hormone Chain: A: PDB Molecule:pancreatic hormone; PDBTitle: anisotropic refinement of avian (turkey) pancreatic2 polypeptide at 0.99 angstroms resolution.
6 | c2nr1A_ |
|  | 7.7 | 100 | PDB header:receptor Chain: A: PDB Molecule:nr1 m2; PDBTitle: transmembrane segment 2 of nmda receptor nr1, nmr, 102 structures
7 | c3gycB_ |
|  | 7.5 | 40 | PDB header:hydrolase Chain: B: PDB Molecule:putative glycoside hydrolase; PDBTitle: crystal structure of putative glycoside hydrolase (yp_001304622.1)2 from parabacteroides distasonis atcc 8503 at 1.85 a resolution
8 | c1wqsA_ |
|  | 7.1 | 71 | PDB header:hydrolase Chain: A: PDB Molecule:3c-like protease; PDBTitle: crystal structure of norovirus 3c-like protease
9 | c3h1sB_ |
|  | 6.9 | 63 | PDB header:oxidoreductase Chain: B: PDB Molecule:superoxide dismutase; PDBTitle: crystal structure of superoxide dismutase from francisella tularensis2 subsp. tularensis schu s4
10 | c2dezA_ |
|  | 6.6 | 55 | PDB header:neuropeptide Chain: A: PDB Molecule:peptide yy; PDBTitle: structure of human pyy
11 | c1dt0A_ |
|  | 6.6 | 75 | PDB header:oxidoreductase Chain: A: PDB Molecule:superoxide dismutase; PDBTitle: cloning, sequence, and crystallographic structure of2 recombinant iron superoxide dismutase from pseudomonas3 ovalis
12 | c1ronA_ |
|  | 6.6 | 64 | PDB header:neuropeptide Chain: A: PDB Molecule:neuropeptide y; PDBTitle: nmr solution structure of human neuropeptide y
13 | c2vdaB_ |
|  | 6.4 | 50 | PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex
14 | d2z0da1 |
|  | 6.2 | 50 | Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Autophagin-like
15 | c2hv8D_ |
|  | 6.2 | 43 | PDB header:protein transport Chain: D: PDB Molecule:rab11 family-interacting protein 3; PDBTitle: crystal structure of gtp-bound rab11 in complex with fip3
16 | c1tz5A_ |
|  | 6.1 | 45 | PDB header:hormone/growth factor Chain: A: PDB Molecule:chimera of pancreatic hormone and neuropeptide y; PDBTitle: [pnpy19-23]-hpp bound to dpc micelles
17 | d1kkca2 |
|  | 5.7 | 75 | Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain
18 | d2j01p1 |
|  | 5.5 | 63 | Fold:Ribosomal proteins L15p and L18e Superfamily:Ribosomal proteins L15p and L18e Family:Ribosomal proteins L15p and L18e
19 | c1qnnD_ |
|  | 5.5 | 63 | PDB header:oxidoreductase Chain: D: PDB Molecule:superoxide dismutase; PDBTitle: cambialistic superoxide dismutase from porphyromonas2 gingivalis
20 | c1my6A_ |
|  | 5.4 | 63 | PDB header:oxidoreductase Chain: A: PDB Molecule:iron (iii) superoxide dismutase; PDBTitle: the 1.6 a structure of fe-superoxide dismutase from the2 thermophilic cyanobacterium thermosynechococcus elongatus3 : correlation of epr and structural characteristics
21 | d3sdpa2 |
| not modelled | 5.3 | 63 | Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain
22 | c3ceiA_ |
| not modelled | 5.3 | 50 | PDB header:oxidoreductase Chain: A: PDB Molecule:superoxide dismutase; PDBTitle: crystal structure of superoxide dismutase from helicobacter2 pylori
23 | d1ix9a2 |
| not modelled | 5.3 | 63 | Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain
24 | c3js4C_ |
| not modelled | 5.2 | 63 | PDB header:oxidoreductase Chain: C: PDB Molecule:superoxide dismutase; PDBTitle: crystal structure of iron superoxide dismutase from anaplasma2 phagocytophilum
25 | d1y67a2 |
| not modelled | 5.2 | 63 | Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain
26 | c3tqjB_ |
| not modelled | 5.2 | 63 | PDB header:oxidoreductase Chain: B: PDB Molecule:superoxide dismutase [fe]; PDBTitle: structure of the superoxide dismutase (fe) (sodb) from coxiella2 burnetii
27 | c2nybC_ |
| not modelled | 5.1 | 63 | PDB header:oxidoreductase Chain: C: PDB Molecule:superoxide dismutase [fe]; PDBTitle: crystal structure of e.coli iron superoxide dismutase q69e2 at 1.1 angstrom resolution
28 | c2a03A_ |
| not modelled | 5.1 | 75 | PDB header:oxidoreductase Chain: A: PDB Molecule:fe-superoxide dismutase homolog; PDBTitle: superoxide dismutase protein from plasmodium berghei

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