Phyre 2 Results for P18032

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Email | l.a.kelley@imperial.ac.uk
Description | P18032
Date | Thu Jan 5 11:36:34 GMT 2012
Unique Job ID | d3f62666f9269689

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c1fqjC_
Top template information
PDB header:signaling protein Chain: C: PDB Molecule:retinal rod rhodopsin-sensitive cgmp 3',5'- PDBTitle: crystal structure of the heterotrimeric complex of the rgs2 domain of rgs9, the gamma subunit of phosphodiesterase and3 the gt/i1 chimera alpha subunit [(rgs9)-(pdegamma)-4 (gt/i1alpha)-(gdp)-(alf4-)-(mg2+)]
Confidence and coverage
Confidence: | 30.4% | Coverage: | 10%
10 residues ( 10% of your sequence) have been modelled with 30.4% 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 | E | K | R | S | F | K | E | K | L | E | I | I | R | N | I | I | R | E | S | L | L | G | N | A | A | I | I | A | L | I | Y | A | A | S | H | S | L | P | V | N | A | F | P | D | Y | L | V | I | S | L | L | S | I | A | A | G | I | V | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | .
Sequence |  | L | W | L | F | S | I | I | Y | I | Y | F | C | E | L | F | R | S | H | W | I | A | V | W | F | I | I | W | S | S | V | I | N | L | I | I | L | Y | G | F | Y | D | R | F | 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 |
| c1fqjC_ |

### PDB 1fqj chain C

Region: 34 - 43
Aligned: 10
Modelled: 10
Confidence: 30.4%
Identity: 30%
PDB header:signaling protein
Chain: C: PDB Molecule:retinal rod rhodopsin-sensitive cgmp 3',5'-
PDBTitle: crystal structure of the heterotrimeric complex of the rgs2 domain of rgs9, the gamma subunit of phosphodiesterase and3 the gt/i1 chimera alpha subunit [(rgs9)-(pdegamma)-4 (gt/i1alpha)-(gdp)-(alf4-)-(mg2+)]

Phyre2
2 |
| c1u3fA_ |

### PDB 1u3f chain A

Region: 98 - 104
Aligned: 7
Modelled: 7
Confidence: 25.4%
Identity: 57%
PDB header:ligase
Chain: A: PDB Molecule:5,10-methenyltetrahydrofolate synthetase;
PDBTitle: structural and functional characterization of a 5,10-2 methenyltetrahydrofolate synthetase from mycoplasma3 pneumoniae (gi: 13508087)

Phyre2
3 |
| d1sbqa_ |

### PDB 1sbq chain A

Region: 98 - 104
Aligned: 7
Modelled: 7
Confidence: 25.4%
Identity: 57%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: Methenyltetrahydrofolate synthetase

Phyre2
4 |
| c2jziB_ |

### PDB 2jzi chain B

Region: 11 - 18
Aligned: 8
Modelled: 8
Confidence: 23.6%
Identity: 75%
PDB header:metal binding protein
Chain: B: PDB Molecule:serine/threonine-protein phosphatase 2b
PDBTitle: structure of calmodulin complexed with the calmodulin2 binding domain of calcineurin

Phyre2
5 |
| c2jcbA_ |

### PDB 2jcb chain A

Region: 98 - 104
Aligned: 7
Modelled: 7
Confidence: 20.0%
Identity: 57%
PDB header:ligase
Chain: A: PDB Molecule:5-formyltetrahydrofolate cyclo-ligase family protein;
PDBTitle: the crystal structure of 5-formyl-tetrahydrofolate2 cycloligase from bacillus anthracis (ba4489)

Phyre2
6 |
| c3hy4A_ |

### PDB 3hy4 chain A

Region: 98 - 104
Aligned: 7
Modelled: 7
Confidence: 19.8%
Identity: 43%
PDB header:ligase
Chain: A: PDB Molecule:5-formyltetrahydrofolate cyclo-ligase;
PDBTitle: structure of human mthfs with n5-iminium phosphate

Phyre2
7 |
| d2hzab1 |

### PDB 2hza chain B domain 1

Region: 11 - 21
Aligned: 11
Modelled: 11
Confidence: 18.2%
Identity: 55%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: CopG-like

Phyre2
8 |
| c2r2vB_ |

### PDB 2r2v chain B

Region: 1 - 11
Aligned: 11
Modelled: 11
Confidence: 18.0%
Identity: 36%
PDB header:de novo protein
Chain: B: PDB Molecule:gcn4 leucine zipper;
PDBTitle: sequence determinants of the topology of the lac repressor2 tetrameric coiled coil

Phyre2
9 |
| d2hzaa1 |

### PDB 2hza chain A domain 1

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 17.3%
Identity: 44%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: CopG-like

Phyre2
10 |
| d1wkca_ |

### PDB 1wkc chain A

Region: 98 - 103
Aligned: 6
Modelled: 6
Confidence: 16.5%
Identity: 100%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: Methenyltetrahydrofolate synthetase

Phyre2
11 |
| c1ydmC_ |

### PDB 1ydm chain C

Region: 98 - 103
Aligned: 6
Modelled: 6
Confidence: 13.7%
Identity: 67%
PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:hypothetical protein yqgn;
PDBTitle: x-ray structure of northeast structural genomics target sr44

Phyre2
12 |
| c2r28D_ |

### PDB 2r28 chain D

Region: 11 - 18
Aligned: 8
Modelled: 8
Confidence: 12.5%
Identity: 75%
PDB header:metal binding protein/hydrolase
Chain: D: PDB Molecule:serine/threonine-protein phosphatase 2b
PDBTitle: the complex structure of calmodulin bound to a calcineurin2 peptide

Phyre2
13 |
| c2kzuA_ |

### PDB 2kzu chain A

Region: 67 - 74
Aligned: 8
Modelled: 8
Confidence: 11.6%
Identity: 50%
PDB header:apoptosis
Chain: A: PDB Molecule:death-associated protein 6;
PDBTitle: daxx helical bundle (dhb) domain / rassf1c complex

Phyre2
14 |
| d2bj7a1 |

### PDB 2bj7 chain A domain 1

Region: 11 - 21
Aligned: 11
Modelled: 11
Confidence: 9.8%
Identity: 45%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: CopG-like

Phyre2
15 |
| d1soua_ |

### PDB 1sou chain A

Region: 98 - 103
Aligned: 6
Modelled: 6
Confidence: 9.6%
Identity: 67%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: Methenyltetrahydrofolate synthetase

Phyre2
16 |
| d2i8da1 |

### PDB 2i8d chain A domain 1

Region: 5 - 21
Aligned: 17
Modelled: 17
Confidence: 9.4%
Identity: 6%
Fold: Secretion chaperone-like
Superfamily: YdhG-like
Family: YdhG-like

Phyre2
17 |
| d1wf3a2 |

### PDB 1wf3 chain A domain 2

Region: 11 - 22
Aligned: 12
Modelled: 12
Confidence: 9.1%
Identity: 33%
Fold: Alpha-lytic protease prodomain-like
Superfamily: Prokaryotic type KH domain (KH-domain type II)
Family: Prokaryotic type KH domain (KH-domain type II)

Phyre2
18 |
| c3rkoK_ |

### PDB 3rko chain K

Region: 12 - 70
Aligned: 57
Modelled: 59
Confidence: 8.4%
Identity: 19%
PDB header:oxidoreductase
Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k;
PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution

Phyre2
19 |
| c2ovmB_ |

### PDB 2ovm chain B

Region: 15 - 26
Aligned: 12
Modelled: 9
Confidence: 8.1%
Identity: 42%
PDB header:transcription
Chain: B: PDB Molecule:ncor;
PDBTitle: progesterone receptor with bound asoprisnil and a peptide2 from the co-repressor ncor

Phyre2
20 |
| d1egaa2 |

### PDB 1ega chain A domain 2

Region: 11 - 24
Aligned: 14
Modelled: 14
Confidence: 7.7%
Identity: 36%
Fold: Alpha-lytic protease prodomain-like
Superfamily: Prokaryotic type KH domain (KH-domain type II)
Family: Prokaryotic type KH domain (KH-domain type II)

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 | c1fqjC_ |
|  | 30.4 | 30 | PDB header:signaling protein Chain: C: PDB Molecule:retinal rod rhodopsin-sensitive cgmp 3',5'- PDBTitle: crystal structure of the heterotrimeric complex of the rgs2 domain of rgs9, the gamma subunit of phosphodiesterase and3 the gt/i1 chimera alpha subunit [(rgs9)-(pdegamma)-4 (gt/i1alpha)-(gdp)-(alf4-)-(mg2+)]
2 | c1u3fA_ |
|  | 25.4 | 57 | PDB header:ligase Chain: A: PDB Molecule:5,10-methenyltetrahydrofolate synthetase; PDBTitle: structural and functional characterization of a 5,10-2 methenyltetrahydrofolate synthetase from mycoplasma3 pneumoniae (gi: 13508087)
3 | d1sbqa_ |
|  | 25.4 | 57 | Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:Methenyltetrahydrofolate synthetase
4 | c2jziB_ |
|  | 23.6 | 75 | PDB header:metal binding protein Chain: B: PDB Molecule:serine/threonine-protein phosphatase 2b PDBTitle: structure of calmodulin complexed with the calmodulin2 binding domain of calcineurin
5 | c2jcbA_ |
|  | 20.0 | 57 | PDB header:ligase Chain: A: PDB Molecule:5-formyltetrahydrofolate cyclo-ligase family protein; PDBTitle: the crystal structure of 5-formyl-tetrahydrofolate2 cycloligase from bacillus anthracis (ba4489)
6 | c3hy4A_ |
|  | 19.8 | 43 | PDB header:ligase Chain: A: PDB Molecule:5-formyltetrahydrofolate cyclo-ligase; PDBTitle: structure of human mthfs with n5-iminium phosphate
7 | d2hzab1 |
|  | 18.2 | 55 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like
8 | c2r2vB_ |
|  | 18.0 | 36 | PDB header:de novo protein Chain: B: PDB Molecule:gcn4 leucine zipper; PDBTitle: sequence determinants of the topology of the lac repressor2 tetrameric coiled coil
9 | d2hzaa1 |
|  | 17.3 | 44 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like
10 | d1wkca_ |
|  | 16.5 | 100 | Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:Methenyltetrahydrofolate synthetase
11 | c1ydmC_ |
|  | 13.7 | 67 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein yqgn; PDBTitle: x-ray structure of northeast structural genomics target sr44
12 | c2r28D_ |
|  | 12.5 | 75 | PDB header:metal binding protein/hydrolase Chain: D: PDB Molecule:serine/threonine-protein phosphatase 2b PDBTitle: the complex structure of calmodulin bound to a calcineurin2 peptide
13 | c2kzuA_ |
|  | 11.6 | 50 | PDB header:apoptosis Chain: A: PDB Molecule:death-associated protein 6; PDBTitle: daxx helical bundle (dhb) domain / rassf1c complex
14 | d2bj7a1 |
|  | 9.8 | 45 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like
15 | d1soua_ |
|  | 9.6 | 67 | Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:Methenyltetrahydrofolate synthetase
16 | d2i8da1 |
|  | 9.4 | 6 | Fold:Secretion chaperone-like Superfamily:YdhG-like Family:YdhG-like
17 | d1wf3a2 |
|  | 9.1 | 33 | Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II)
18 | c3rkoK_ |
|  | 8.4 | 19 | PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution
19 | c2ovmB_ |
|  | 8.1 | 42 | PDB header:transcription Chain: B: PDB Molecule:ncor; PDBTitle: progesterone receptor with bound asoprisnil and a peptide2 from the co-repressor ncor
20 | d1egaa2 |
|  | 7.7 | 36 | Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II)
21 | d1aoya_ |
| not modelled | 7.5 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
22 | c2ksdA_ |
| not modelled | 7.2 | 19 | PDB header:transferase Chain: A: PDB Molecule:aerobic respiration control sensor protein arcb; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor arcb, center for structures of3 membrane proteins (csmp) target 4310c
23 | d1qlec_ |
| not modelled | 6.6 | 20 | Fold:Cytochrome c oxidase subunit III-like Superfamily:Cytochrome c oxidase subunit III-like Family:Cytochrome c oxidase subunit III-like
24 | c2yggA_ |
| not modelled | 6.4 | 44 | PDB header:metal binding protein/transport protein Chain: A: PDB Molecule:sodium/hydrogen exchanger 1; PDBTitle: complex of cambr and cam
25 | d1vp6a_ |
| not modelled | 6.1 | 6 | Fold:Double-stranded beta-helix Superfamily:cAMP-binding domain-like Family:cAMP-binding domain
26 | c2voiB_ |
| not modelled | 6.1 | 75 | PDB header:apoptosis Chain: B: PDB Molecule:bh3-interacting domain death agonist p13; PDBTitle: structure of mouse a1 bound to the bid bh3-domain
27 | c2kjrA_ |
| not modelled | 5.9 | 38 | PDB header:chaperone Chain: A: PDB Molecule:cg11242; PDBTitle: solution nmr structure of the n-terminal ubiquitin-like2 domain from tubulin-binding cofactor b, cg11242, from3 drosophila melanogaster. northeast structural genomics4 consortium target fr629a (residues 8-92)
28 | c1usdA_ |
| not modelled | 5.3 | 37 | PDB header:signaling protein Chain: A: PDB Molecule:vasodilator-stimulated phosphoprotein; PDBTitle: human vasp tetramerisation domain l352m
29 | c1lt1G_ |
| not modelled | 5.2 | 20 | PDB header:de novo protein Chain: G: PDB Molecule:l13g-df1; PDBTitle: sliding helix induced change of coordination geometry in a2 model di-mn(ii) protein
30 | c1q5vB_ |
| not modelled | 5.1 | 55 | PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr

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