Phyre 2 Results for P77656

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Email | l.a.kelley@imperial.ac.uk
Description | P77656
Date | Thu Jan 5 12:31:23 GMT 2012
Unique Job ID | 3b49cbf9ba08b973

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2kz6A_
Top template information
PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of protein cv0426 from chromobacterium violaceum,2 northeast structural genomics consortium (nesg) target cvt2
Confidence and coverage
Confidence: | 98.4% | Coverage: | 42%
61 residues ( 42% of your sequence) have been modelled with 98.4% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | N | Y | I | Y | S | A | T | T | N | S | F | Y | P | L | E | M | K | E | D | Y | T | Q | A | G | S | W | P | D | D | A | V | E | V | D | E | Q | V | Y | I | E | F | S | G | L | P | P | K | G | K | I | R | I | A | G | E | N | G | F | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | A | W | S | E | I | P | P | P | T | H | E | E | Q | I | A | A | A | E | L | K | K | Q | Q | L | I | N | Q | A | N | D | Y | M | N | S | K | Q | W | A | G | K | A | A | I | G | R | L | K | G | E | E | L | A | Q | Y | N | L | W | L | D | Y
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  |  |  | ? |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | .
Sequence |  | L | D | A | L | E | L | V | D | T | S | S | A | P | D | I | E | W | P | T | P | P | A | V | Q | A | R
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 |
| c2kz6A_ |

### PDB 2kz6 chain A

Region: 70 - 141
Aligned: 61
Modelled: 72
Confidence: 98.4%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: solution structure of protein cv0426 from chromobacterium violaceum,2 northeast structural genomics consortium (nesg) target cvt2

Phyre2
2 |
| c3o0rC_ |

### PDB 3o0r chain C

Region: 106 - 133
Aligned: 25
Modelled: 28
Confidence: 28.1%
Identity: 20%
PDB header:immune system/oxidoreductase
Chain: C: PDB Molecule:nitric oxide reductase subunit c;
PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment

Phyre2
3 |
| d1y2oa1 |

### PDB 1y2o chain A domain 1

Region: 71 - 126
Aligned: 56
Modelled: 56
Confidence: 26.3%
Identity: 13%
Fold: BAR/IMD domain-like
Superfamily: BAR/IMD domain-like
Family: IMD domain

Phyre2
4 |
| d1x4ta1 |

### PDB 1x4t chain A domain 1

Region: 58 - 116
Aligned: 53
Modelled: 59
Confidence: 21.4%
Identity: 21%
Fold: Long alpha-hairpin
Superfamily: ISY1 domain-like
Family: ISY1 N-terminal domain-like

Phyre2
5 |
| c1fcuA_ |

### PDB 1fcu chain A

Region: 1 - 63
Aligned: 60
Modelled: 63
Confidence: 21.1%
Identity: 15%
PDB header:hydrolase
Chain: A: PDB Molecule:hyaluronoglucosaminidase;
PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase

Phyre2
6 |
| d1fcqa_ |

### PDB 1fcq chain A

Region: 1 - 80
Aligned: 74
Modelled: 77
Confidence: 19.7%
Identity: 18%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: Bee venom hyaluronidase

Phyre2
7 |
| c3ok8A_ |

### PDB 3ok8 chain A

Region: 71 - 126
Aligned: 56
Modelled: 56
Confidence: 16.5%
Identity: 11%
PDB header:protein binding
Chain: A: PDB Molecule:brain-specific angiogenesis inhibitor 1-associated protein
PDBTitle: i-bar of pinkbar

Phyre2
8 |
| d2fiqa1 |

### PDB 2fiq chain A domain 1

Region: 20 - 86
Aligned: 63
Modelled: 67
Confidence: 15.4%
Identity: 17%
Fold: TIM beta/alpha-barrel
Superfamily: Aldolase
Family: GatZ-like

Phyre2
9 |
| c2clyE_ |

### PDB 2cly chain E

Region: 105 - 137
Aligned: 33
Modelled: 33
Confidence: 13.3%
Identity: 15%
PDB header:hydrolase
Chain: E: PDB Molecule:atp synthase d chain, mitochondrial;
PDBTitle: subcomplex of the stator of bovine mitochondrial atp2 synthase

Phyre2
10 |
| d2gu3a1 |

### PDB 2gu3 chain A domain 1

Region: 34 - 62
Aligned: 29
Modelled: 29
Confidence: 12.7%
Identity: 10%
Fold: Cystatin-like
Superfamily: Cystatin/monellin
Family: PepSY-like

Phyre2
11 |
| c2w56B_ |

### PDB 2w56 chain B

Region: 5 - 27
Aligned: 23
Modelled: 23
Confidence: 10.2%
Identity: 43%
PDB header:unknown function
Chain: B: PDB Molecule:vc0508;
PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island

Phyre2
12 |
| d2clyb1 |

### PDB 2cly chain B domain 1

Region: 105 - 137
Aligned: 33
Modelled: 33
Confidence: 9.3%
Identity: 15%
Fold: ATP synthase D chain-like
Superfamily: ATP synthase D chain-like
Family: ATP synthase D chain-like

Phyre2
13 |
| c2atmA_ |

### PDB 2atm chain A

Region: 1 - 63
Aligned: 60
Modelled: 60
Confidence: 9.1%
Identity: 15%
PDB header:hydrolase
Chain: A: PDB Molecule:hyaluronoglucosaminidase;
PDBTitle: crystal structure of the recombinant allergen ves v 2

Phyre2
14 |
| c2ahmG_ |

### PDB 2ahm chain G

Region: 122 - 138
Aligned: 17
Modelled: 17
Confidence: 8.4%
Identity: 24%
PDB header:viral protein, replication
Chain: G: PDB Molecule:replicase polyprotein 1ab, heavy chain;
PDBTitle: crystal structure of sars-cov super complex of non-structural2 proteins: the hexadecamer

Phyre2
15 |
| c2v1lA_ |

### PDB 2v1l chain A

Region: 5 - 27
Aligned: 23
Modelled: 23
Confidence: 8.1%
Identity: 35%
PDB header:unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: structure of the conserved hypothetical protein vc1805 from2 pathogenicity island vpi-2 of vibrio cholerae o1 biovar3 eltor str. n16961 shares structural homology with the4 human p32 protein

Phyre2
16 |
| d1bgva2 |

### PDB 1bgv chain A domain 2

Region: 106 - 130
Aligned: 25
Modelled: 25
Confidence: 7.6%
Identity: 8%
Fold: Aminoacid dehydrogenase-like, N-terminal domain
Superfamily: Aminoacid dehydrogenase-like, N-terminal domain
Family: Aminoacid dehydrogenases

Phyre2
17 |
| d1lrza2 |

### PDB 1lrz chain A domain 2

Region: 32 - 49
Aligned: 18
Modelled: 18
Confidence: 7.4%
Identity: 11%
Fold: Acyl-CoA N-acyltransferases (Nat)
Superfamily: Acyl-CoA N-acyltransferases (Nat)
Family: FemXAB nonribosomal peptidyltransferases

Phyre2
18 |
| c2odkD_ |

### PDB 2odk chain D

Region: 39 - 77
Aligned: 39
Modelled: 39
Confidence: 6.9%
Identity: 21%
PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:hypothetical protein;
PDBTitle: putative prevent-host-death protein from nitrosomonas europaea

Phyre2
19 |
| d2q22a1 |

### PDB 2q22 chain A domain 1

Region: 78 - 139
Aligned: 58
Modelled: 62
Confidence: 6.7%
Identity: 14%
Fold: Ava3019-like
Superfamily: Ava3019-like
Family: Ava3019-like

Phyre2
20 |
| d1zaka2 |

### PDB 1zak chain A domain 2

Region: 136 - 146
Aligned: 11
Modelled: 11
Confidence: 6.7%
Identity: 18%
Fold: Rubredoxin-like
Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
Family: Microbial and mitochondrial ADK, insert "zinc finger" 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 | c2kz6A_ |
|  | 98.4 | 18 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of protein cv0426 from chromobacterium violaceum,2 northeast structural genomics consortium (nesg) target cvt2
2 | c3o0rC_ |
|  | 28.1 | 20 | PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment
3 | d1y2oa1 |
|  | 26.3 | 13 | Fold:BAR/IMD domain-like Superfamily:BAR/IMD domain-like Family:IMD domain
4 | d1x4ta1 |
|  | 21.4 | 21 | Fold:Long alpha-hairpin Superfamily:ISY1 domain-like Family:ISY1 N-terminal domain-like
5 | c1fcuA_ |
|  | 21.1 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase
6 | d1fcqa_ |
|  | 19.7 | 18 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Bee venom hyaluronidase
7 | c3ok8A_ |
|  | 16.5 | 11 | PDB header:protein binding Chain: A: PDB Molecule:brain-specific angiogenesis inhibitor 1-associated protein PDBTitle: i-bar of pinkbar
8 | d2fiqa1 |
|  | 15.4 | 17 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:GatZ-like
9 | c2clyE_ |
|  | 13.3 | 15 | PDB header:hydrolase Chain: E: PDB Molecule:atp synthase d chain, mitochondrial; PDBTitle: subcomplex of the stator of bovine mitochondrial atp2 synthase
10 | d2gu3a1 |
|  | 12.7 | 10 | Fold:Cystatin-like Superfamily:Cystatin/monellin Family:PepSY-like
11 | c2w56B_ |
|  | 10.2 | 43 | PDB header:unknown function Chain: B: PDB Molecule:vc0508; PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island
12 | d2clyb1 |
|  | 9.3 | 15 | Fold:ATP synthase D chain-like Superfamily:ATP synthase D chain-like Family:ATP synthase D chain-like
13 | c2atmA_ |
|  | 9.1 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure of the recombinant allergen ves v 2
14 | c2ahmG_ |
|  | 8.4 | 24 | PDB header:viral protein, replication Chain: G: PDB Molecule:replicase polyprotein 1ab, heavy chain; PDBTitle: crystal structure of sars-cov super complex of non-structural2 proteins: the hexadecamer
15 | c2v1lA_ |
|  | 8.1 | 35 | PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of the conserved hypothetical protein vc1805 from2 pathogenicity island vpi-2 of vibrio cholerae o1 biovar3 eltor str. n16961 shares structural homology with the4 human p32 protein
16 | d1bgva2 |
|  | 7.6 | 8 | Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases
17 | d1lrza2 |
|  | 7.4 | 11 | Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:FemXAB nonribosomal peptidyltransferases
18 | c2odkD_ |
|  | 6.9 | 21 | PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: putative prevent-host-death protein from nitrosomonas europaea
19 | d2q22a1 |
|  | 6.7 | 14 | Fold:Ava3019-like Superfamily:Ava3019-like Family:Ava3019-like
20 | d1zaka2 |
|  | 6.7 | 18 | Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
21 | d2ahme1 |
| not modelled | 6.2 | 24 | Fold:Coronavirus NSP8-like Superfamily:Coronavirus NSP8-like Family:Coronavirus NSP8-like
22 | d2pbza2 |
| not modelled | 6.1 | 17 | Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:PurP ATP-binding domain-like
23 | d1zs4a1 |
| not modelled | 5.6 | 12 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Bacteriophage CII protein
24 | d2odka1 |
| not modelled | 5.5 | 21 | Fold:YefM-like Superfamily:YefM-like Family:YefM-like
25 | c1p9cA_ |
| not modelled | 5.5 | 32 | PDB header:ligand binding protein Chain: A: PDB Molecule:26s proteasome non-atpase regulatory subunit 4; PDBTitle: nmr solution structure of the c-terminal ubiquitin-2 interacting motif of the proteasome subunit s5a
26 | d1k4na_ |
| not modelled | 5.3 | 11 | Fold:Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Superfamily:Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Family:Hypothetical protein YecM (EC4020)
27 | d1nira1 |
| not modelled | 5.2 | 18 | Fold:Cytochrome c Superfamily:Cytochrome c Family:N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
28 | d2hq9a1 |
| not modelled | 5.2 | 15 | Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like
29 | d2fg9a1 |
| not modelled | 5.1 | 13 | Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase 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
Disclaimer
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