Phyre 2 Results for P0A8Q0

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Email | l.a.kelley@imperial.ac.uk
Description | P0A8Q0
Date | Wed Jan 25 15:20:18 GMT 2012
Unique Job ID | e0ed5233a5c75ad3

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1kf6c_
Top template information
Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
Confidence and coverage
Confidence: | 100.0% | Coverage: | 99%
130 residues ( 99% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | T | T | K | R | K | P | Y | V | R | P | M | T | S | T | W | W | K | K | L | P | F | Y | R | F | Y | M | L | R | E | G | T | A | V | P | A | V | W | F | S | I | E | L | I | F | G | L | F | A | L | K | N | G | P | E | A | W | A | G | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | V | D | F | L | Q | N | P | V | I | V | I | I | N | L | I | T | L | A | A | A | L | L | H | T | K | T | W | F | E | L | A | P | K | A | A | N | I | I | V | K | D | E | K | M | G | P | E | P | I | I | K | S | L | W | A | V | T | V | V | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | .
Sequence |  | T | I | V | I | L | F | V | A | L | Y | W
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 |
| d1kf6c_ |

### PDB 1kf6 chain C

Region: 2 - 131
Aligned: 130
Modelled: 130
Confidence: 100.0%
Identity: 100%
Fold: Heme-binding four-helical bundle
Superfamily: Fumarate reductase respiratory complex transmembrane subunits
Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)

Phyre2
2 |
| d1nekd_ |

### PDB 1nek chain D

Region: 24 - 130
Aligned: 97
Modelled: 107
Confidence: 96.8%
Identity: 20%
Fold: Heme-binding four-helical bundle
Superfamily: Fumarate reductase respiratory complex transmembrane subunits
Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)

Phyre2
3 |
| d1nekc_ |

### PDB 1nek chain C

Region: 28 - 130
Aligned: 96
Modelled: 103
Confidence: 89.7%
Identity: 15%
Fold: Heme-binding four-helical bundle
Superfamily: Fumarate reductase respiratory complex transmembrane subunits
Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)

Phyre2
4 |
| d1kf6d_ |

### PDB 1kf6 chain D

Region: 32 - 129
Aligned: 89
Modelled: 98
Confidence: 75.1%
Identity: 17%
Fold: Heme-binding four-helical bundle
Superfamily: Fumarate reductase respiratory complex transmembrane subunits
Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)

Phyre2
5 |
| c1yq3C_ |

### PDB 1yq3 chain C

Region: 28 - 129
Aligned: 97
Modelled: 102
Confidence: 68.7%
Identity: 13%
PDB header:oxidoreductase
Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit;
PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone

Phyre2
6 |
| d2bs2c1 |

### PDB 2bs2 chain C domain 1

Region: 18 - 130
Aligned: 113
Modelled: 113
Confidence: 32.7%
Identity: 12%
Fold: Heme-binding four-helical bundle
Superfamily: Fumarate reductase respiratory complex transmembrane subunits
Family: Fumarate reductase respiratory complex cytochrome b subunit, FrdC

Phyre2
7 |
| c2b1wA_ |

### PDB 2b1w chain A

Region: 51 - 70
Aligned: 20
Modelled: 20
Confidence: 26.6%
Identity: 30%
PDB header:apoptosis
Chain: A: PDB Molecule:caspase recruitment domain protein 4;
PDBTitle: solution structure of the nod1 caspase activating and recruitment2 domain

Phyre2
8 |
| d1lg7a_ |

### PDB 1lg7 chain A

Region: 19 - 29
Aligned: 11
Modelled: 11
Confidence: 23.7%
Identity: 36%
Fold: VSV matrix protein
Superfamily: VSV matrix protein
Family: VSV matrix protein

Phyre2
9 |
| c2w2rA_ |

### PDB 2w2r chain A

Region: 19 - 29
Aligned: 11
Modelled: 11
Confidence: 20.5%
Identity: 45%
PDB header:viral protein
Chain: A: PDB Molecule:matrix protein;
PDBTitle: structure of the vesicular stomatitis virus matrix protein

Phyre2
10 |
| d3ygsp_ |

### PDB 3ygs chain P

Region: 51 - 66
Aligned: 16
Modelled: 16
Confidence: 20.0%
Identity: 25%
Fold: DEATH domain
Superfamily: DEATH domain
Family: Caspase recruitment domain, CARD

Phyre2
11 |
| c2nz7A_ |

### PDB 2nz7 chain A

Region: 51 - 65
Aligned: 15
Modelled: 15
Confidence: 19.0%
Identity: 33%
PDB header:apoptosis
Chain: A: PDB Molecule:caspase recruitment domain-containing protein 4;
PDBTitle: crystal structure analysis of caspase-recruitment domain2 (card) of nod1

Phyre2
12 |
| c3katA_ |

### PDB 3kat chain A

Region: 51 - 65
Aligned: 15
Modelled: 15
Confidence: 17.5%
Identity: 13%
PDB header:apoptosis
Chain: A: PDB Molecule:nacht, lrr and pyd domains-containing protein 1;
PDBTitle: crystal structure of the card domain of the human nlrp12 protein, northeast structural genomics consortium target3 hr3486e

Phyre2
13 |
| d3crda_ |

### PDB 3crd chain A

Region: 51 - 66
Aligned: 16
Modelled: 16
Confidence: 15.4%
Identity: 44%
Fold: DEATH domain
Superfamily: DEATH domain
Family: Caspase recruitment domain, CARD

Phyre2
14 |
| d1dgna_ |

### PDB 1dgn chain A

Region: 51 - 66
Aligned: 16
Modelled: 16
Confidence: 14.1%
Identity: 25%
Fold: DEATH domain
Superfamily: DEATH domain
Family: Caspase recruitment domain, CARD

Phyre2
15 |
| c2kxwB_ |

### PDB 2kxw chain B

Region: 21 - 29
Aligned: 9
Modelled: 9
Confidence: 13.5%
Identity: 44%
PDB header:calcium-binding protein/metal transport
Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha;
PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2

Phyre2
16 |
| d1y9ba1 |

### PDB 1y9b chain A domain 1

Region: 53 - 67
Aligned: 15
Modelled: 15
Confidence: 12.7%
Identity: 20%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: VCA0319-like

Phyre2
17 |
| c1p58F_ |

### PDB 1p58 chain F

Region: 15 - 46
Aligned: 32
Modelled: 32
Confidence: 11.8%
Identity: 16%
PDB header:virus
Chain: F: PDB Molecule:envelope protein m;
PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction

Phyre2
18 |
| c2q0oC_ |

### PDB 2q0o chain C

Region: 50 - 67
Aligned: 18
Modelled: 18
Confidence: 10.9%
Identity: 11%
PDB header:transcription
Chain: C: PDB Molecule:probable transcriptional repressor tram;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing

Phyre2
19 |
| c2h3oA_ |

### PDB 2h3o chain A

Region: 41 - 81
Aligned: 37
Modelled: 41
Confidence: 9.9%
Identity: 24%
PDB header:membrane protein
Chain: A: PDB Molecule:merf;
PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices

Phyre2
20 |
| d1cy5a_ |

### PDB 1cy5 chain A

Region: 51 - 66
Aligned: 16
Modelled: 16
Confidence: 9.7%
Identity: 19%
Fold: DEATH domain
Superfamily: DEATH domain
Family: Caspase recruitment domain, CARD

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1kf6c_ |
|  | 100.0 | 100 | Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
2 | d1nekd_ |
|  | 96.8 | 20 | Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
3 | d1nekc_ |
|  | 89.7 | 15 | Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
4 | d1kf6d_ |
|  | 75.1 | 17 | Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
5 | c1yq3C_ |
|  | 68.7 | 13 | PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone
6 | d2bs2c1 |
|  | 32.7 | 12 | Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Fumarate reductase respiratory complex cytochrome b subunit, FrdC
7 | c2b1wA_ |
|  | 26.6 | 30 | PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain protein 4; PDBTitle: solution structure of the nod1 caspase activating and recruitment2 domain
8 | d1lg7a_ |
|  | 23.7 | 36 | Fold:VSV matrix protein Superfamily:VSV matrix protein Family:VSV matrix protein
9 | c2w2rA_ |
|  | 20.5 | 45 | PDB header:viral protein Chain: A: PDB Molecule:matrix protein; PDBTitle: structure of the vesicular stomatitis virus matrix protein
10 | d3ygsp_ |
|  | 20.0 | 25 | Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD
11 | c2nz7A_ |
|  | 19.0 | 33 | PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain-containing protein 4; PDBTitle: crystal structure analysis of caspase-recruitment domain2 (card) of nod1
12 | c3katA_ |
|  | 17.5 | 13 | PDB header:apoptosis Chain: A: PDB Molecule:nacht, lrr and pyd domains-containing protein 1; PDBTitle: crystal structure of the card domain of the human nlrp12 protein, northeast structural genomics consortium target3 hr3486e
13 | d3crda_ |
|  | 15.4 | 44 | Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD
14 | d1dgna_ |
|  | 14.1 | 25 | Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD
15 | c2kxwB_ |
|  | 13.5 | 44 | PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2
16 | d1y9ba1 |
|  | 12.7 | 20 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VCA0319-like
17 | c1p58F_ |
|  | 11.8 | 16 | PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction
18 | c2q0oC_ |
|  | 10.9 | 11 | PDB header:transcription Chain: C: PDB Molecule:probable transcriptional repressor tram; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
19 | c2h3oA_ |
|  | 9.9 | 24 | PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices
20 | d1cy5a_ |
|  | 9.7 | 19 | Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD
21 | d1bw6a_ |
| not modelled | 9.5 | 38 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding
22 | c1wazA_ |
| not modelled | 8.4 | 24 | PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles
23 | d2axtk1 |
| not modelled | 7.9 | 38 | Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein K, PsbK Family:PsbK-like
24 | c2y69W_ |
| not modelled | 7.1 | 19 | PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen
25 | d1kcfa2 |
| not modelled | 7.0 | 23 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Mitochondrial resolvase ydc2 catalytic domain
26 | c2voyB_ |
| not modelled | 6.9 | 15 | PDB header:hydrolase Chain: B: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus
27 | c1kcfB_ |
| not modelled | 6.0 | 23 | PDB header:hydrolase Chain: B: PDB Molecule:hypothetical 30.2 kd protein c25g10.02 in PDBTitle: crystal structure of the yeast mitochondrial holliday2 junction resolvase, ydc2
28 | c2l9mA_ |
| not modelled | 5.9 | 28 | PDB header:apoptosis inhibitor Chain: A: PDB Molecule:baculoviral iap repeat-containing protein 2; PDBTitle: structure of ciap1 card
29 | d1ic8a2 |
| not modelled | 5.9 | 30 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain
30 | c2zidA_ |
| not modelled | 5.4 | 42 | PDB header:hydrolase Chain: A: PDB Molecule:dextran glucosidase; PDBTitle: crystal structure of dextran glucosidase e236q complex with2 isomaltotriose

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