Phyre 2 Results for P37614

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Email | l.a.kelley@imperial.ac.uk
Description | P37614
Date | Thu Jan 5 11:55:50 GMT 2012
Unique Job ID | d97a30cacb120d05

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3lw52_
Top template information
PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from photosystem i; PDB Fragment:residues 81-246; PDBTitle: improved model of plant photosystem i
Confidence and coverage
Confidence: | 56.2% | Coverage: | 27%
24 residues ( 27% of your sequence) have been modelled with 56.2% confidence by the single highest scoring template.
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | L | I | N | I | G | R | L | L | M | L | C | V | W | G | F | L | I | L | N | L | V | H | P | F | P | R | P | L | N | I | F | V | N | V | A | L | I | F | T | V | L | M | H | G | M | Q | L | A | L | L | K | S | T | L | P | K | D | G | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | .
Sequence |  | Q | M | T | T | A | E | K | V | R | I | F | L | F | G | V | F | E | L | L | A | W | Q | K | K | F | K | V | K | K
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 |
| c3lw52_ |

### PDB 3lw5 chain 2

Region: 3 - 26
Aligned: 24
Modelled: 24
Confidence: 56.2%
Identity: 21%
PDB header:photosynthesis
Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from photosystem i;
PDB Fragment:residues 81-246; PDBTitle: improved model of plant photosystem i

Phyre2
2 |
| c2wsf2_ |

### PDB 2wsf chain 2

Region: 3 - 26
Aligned: 24
Modelled: 24
Confidence: 54.2%
Identity: 21%
PDB header:photosynthesis
Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from
PDBTitle: improved model of plant photosystem i

Phyre2
3 |
| c2wse4_ |

### PDB 2wse chain 4

Region: 3 - 26
Aligned: 24
Modelled: 24
Confidence: 50.6%
Identity: 29%
PDB header:photosynthesis
Chain: 4: PDB Molecule:chlorophyll a-b binding protein p4,
PDBTitle: improved model of plant photosystem i

Phyre2
4 |
| c3pl9A_ |

### PDB 3pl9 chain A

Region: 3 - 26
Aligned: 24
Modelled: 24
Confidence: 48.6%
Identity: 25%
PDB header:photosynthesis
Chain: A: PDB Molecule:chlorophyll a-b binding protein;
PDBTitle: crystal structure of spinach minor light-harvesting complex cp29 at2 2.80 angstrom resolution

Phyre2
5 |
| d1rwta_ |

### PDB 1rwt chain A

Region: 3 - 22
Aligned: 20
Modelled: 20
Confidence: 48.3%
Identity: 40%
Fold: Chlorophyll a-b binding protein
Superfamily: Chlorophyll a-b binding protein
Family: Chlorophyll a-b binding protein

Phyre2
6 |
| c2wse3_ |

### PDB 2wse chain 3

Region: 3 - 17
Aligned: 15
Modelled: 15
Confidence: 36.3%
Identity: 40%
PDB header:photosynthesis
Chain: 3: PDB Molecule:lhca3;
PDBTitle: improved model of plant photosystem i

Phyre2
7 |
| c2o011_ |

### PDB 2o01 chain 1

Region: 3 - 18
Aligned: 16
Modelled: 16
Confidence: 35.0%
Identity: 44%
PDB header:photosynthesis
Chain: 1: PDB Molecule:at3g54890;
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

Phyre2
8 |
| c2o014_ |

### PDB 2o01 chain 4

Region: 3 - 26
Aligned: 24
Modelled: 24
Confidence: 34.4%
Identity: 29%
PDB header:photosynthesis
Chain: 4: PDB Molecule:psi light-harvesting antenna chlorophyll a/b-
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

Phyre2
9 |
| c2o012_ |

### PDB 2o01 chain 2

Region: 3 - 26
Aligned: 24
Modelled: 24
Confidence: 31.9%
Identity: 21%
PDB header:photosynthesis
Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

Phyre2
10 |
| c3brvB_ |

### PDB 3brv chain B

Region: 77 - 89
Aligned: 13
Modelled: 13
Confidence: 31.3%
Identity: 38%
PDB header:transferase/transcription
Chain: B: PDB Molecule:nf-kappa-b essential modulator;
PDBTitle: nemo/ikkb association domain structure

Phyre2
11 |
| c1afoB_ |

### PDB 1afo chain B

Region: 21 - 45
Aligned: 20
Modelled: 25
Confidence: 31.2%
Identity: 40%
PDB header:integral membrane protein
Chain: B: PDB Molecule:glycophorin a;
PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures

Phyre2
12 |
| c2o013_ |

### PDB 2o01 chain 3

Region: 3 - 18
Aligned: 16
Modelled: 16
Confidence: 24.1%
Identity: 44%
PDB header:photosynthesis
Chain: 3: PDB Molecule:psi type iii chlorophyll a/b-binding protein;
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

Phyre2
13 |
| c2wsc1_ |

### PDB 2wsc chain 1

Region: 3 - 18
Aligned: 16
Modelled: 16
Confidence: 19.9%
Identity: 44%
PDB header:photosynthesis
Chain: 1: PDB Molecule:at3g54890;
PDBTitle: improved model of plant photosystem i

Phyre2
14 |
| c2q7cC_ |

### PDB 2q7c chain C

Region: 5 - 15
Aligned: 11
Modelled: 11
Confidence: 12.7%
Identity: 64%
PDB header:viral protein
Chain: C: PDB Molecule:fusion protein between yeast variant gcn4 and
PDBTitle: crystal structure of iqn17

Phyre2
15 |
| c2h3oA_ |

### PDB 2h3o chain A

Region: 70 - 81
Aligned: 12
Modelled: 12
Confidence: 8.4%
Identity: 42%
PDB header:membrane protein
Chain: A: PDB Molecule:merf;
PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices

Phyre2
16 |
| c1wazA_ |

### PDB 1waz chain A

Region: 70 - 81
Aligned: 12
Modelled: 12
Confidence: 8.1%
Identity: 42%
PDB header:transport protein
Chain: A: PDB Molecule:merf;
PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles

Phyre2
17 |
| c2vxoB_ |

### PDB 2vxo chain B

Region: 23 - 28
Aligned: 6
Modelled: 6
Confidence: 7.5%
Identity: 83%
PDB header:ligase
Chain: B: PDB Molecule:gmp synthase [glutamine-hydrolyzing];
PDBTitle: human gmp synthetase in complex with xmp

Phyre2
18 |
| c3cyoA_ |

### PDB 3cyo chain A

Region: 8 - 15
Aligned: 8
Modelled: 8
Confidence: 6.6%
Identity: 75%
PDB header:viral protein
Chain: A: PDB Molecule:transmembrane protein;
PDBTitle: structure of a longer thermalstable core domain of hiv-12 gp41 containing the enfuvirtide resistance mutation n43d3 and complementary mutation e137k

Phyre2
19 |
| c3o3zA_ |

### PDB 3o3z chain A

Region: 8 - 15
Aligned: 8
Modelled: 8
Confidence: 5.7%
Identity: 75%
PDB header:viral protein
Chain: A: PDB Molecule:envelope glycoprotein gp160;
PDBTitle: complex of a chimeric alpha/beta-peptide based on the gp41 chr domain2 bound to a gp41 nhr domain peptide

Phyre2
20 |
| c3uowB_ |

### PDB 3uow chain B

Region: 23 - 28
Aligned: 6
Modelled: 6
Confidence: 5.7%
Identity: 83%
PDB header:ligase
Chain: B: PDB Molecule:gmp synthetase;
PDBTitle: crystal structure of pf10_0123, a gmp synthetase from plasmodium2 falciparum

Phyre2
21 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3lw52_ |
|  | 56.2 | 21 | PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from photosystem i; PDB Fragment:residues 81-246; PDBTitle: improved model of plant photosystem i
2 | c2wsf2_ |
|  | 54.2 | 21 | PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from PDBTitle: improved model of plant photosystem i
3 | c2wse4_ |
|  | 50.6 | 29 | PDB header:photosynthesis Chain: 4: PDB Molecule:chlorophyll a-b binding protein p4, PDBTitle: improved model of plant photosystem i
4 | c3pl9A_ |
|  | 48.6 | 25 | PDB header:photosynthesis Chain: A: PDB Molecule:chlorophyll a-b binding protein; PDBTitle: crystal structure of spinach minor light-harvesting complex cp29 at2 2.80 angstrom resolution
5 | d1rwta_ |
|  | 48.3 | 40 | Fold:Chlorophyll a-b binding protein Superfamily:Chlorophyll a-b binding protein Family:Chlorophyll a-b binding protein
6 | c2wse3_ |
|  | 36.3 | 40 | PDB header:photosynthesis Chain: 3: PDB Molecule:lhca3; PDBTitle: improved model of plant photosystem i
7 | c2o011_ |
|  | 35.0 | 44 | PDB header:photosynthesis Chain: 1: PDB Molecule:at3g54890; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
8 | c2o014_ |
|  | 34.4 | 29 | PDB header:photosynthesis Chain: 4: PDB Molecule:psi light-harvesting antenna chlorophyll a/b- PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
9 | c2o012_ |
|  | 31.9 | 21 | PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
10 | c3brvB_ |
|  | 31.3 | 38 | PDB header:transferase/transcription Chain: B: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: nemo/ikkb association domain structure
11 | c1afoB_ |
|  | 31.2 | 40 | PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures
12 | c2o013_ |
|  | 24.1 | 44 | PDB header:photosynthesis Chain: 3: PDB Molecule:psi type iii chlorophyll a/b-binding protein; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
13 | c2wsc1_ |
|  | 19.9 | 44 | PDB header:photosynthesis Chain: 1: PDB Molecule:at3g54890; PDBTitle: improved model of plant photosystem i
14 | c2q7cC_ |
|  | 12.7 | 64 | PDB header:viral protein Chain: C: PDB Molecule:fusion protein between yeast variant gcn4 and PDBTitle: crystal structure of iqn17
15 | c2h3oA_ |
|  | 8.4 | 42 | PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices
16 | c1wazA_ |
|  | 8.1 | 42 | PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles
17 | c2vxoB_ |
|  | 7.5 | 83 | PDB header:ligase Chain: B: PDB Molecule:gmp synthase [glutamine-hydrolyzing]; PDBTitle: human gmp synthetase in complex with xmp
18 | c3cyoA_ |
|  | 6.6 | 75 | PDB header:viral protein Chain: A: PDB Molecule:transmembrane protein; PDBTitle: structure of a longer thermalstable core domain of hiv-12 gp41 containing the enfuvirtide resistance mutation n43d3 and complementary mutation e137k
19 | c3o3zA_ |
|  | 5.7 | 75 | PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein gp160; PDBTitle: complex of a chimeric alpha/beta-peptide based on the gp41 chr domain2 bound to a gp41 nhr domain peptide
20 | c3uowB_ |
|  | 5.7 | 83 | PDB header:ligase Chain: B: PDB Molecule:gmp synthetase; PDBTitle: crystal structure of pf10_0123, a gmp synthetase from plasmodium2 falciparum
21 | d1h41a2 |
| not modelled | 5.3 | 56 | Fold:Zincin-like Superfamily:beta-N-acetylhexosaminidase-like domain Family:alpha-D-glucuronidase, N-terminal domain

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