Phyre 2 Results for P38394

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Email | l.a.kelley@imperial.ac.uk
Description | P38394
Date | Thu Jan 5 11:58:08 GMT 2012
Unique Job ID | 05a29e5ba3fd1def

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1jjda_
Top template information
Fold:Metallothionein Superfamily:Metallothionein Family:Metallothionein
Confidence and coverage
Confidence: | 33.3% | Coverage: | 27%
15 residues ( 27% of your sequence) have been modelled with 33.3% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

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Sequence |  | M | T | K | K | I | K | C | A | Y | H | L | C | K | K | D | V | E | E | S | K | A | I | E | R | M | L | H | F | M | H | G | I | L | S | K | D | E | P | R | K | Y | C | S | E | A | C | A | E | K | D | Q | M | A | H | E | L
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 |
| d1jjda_ |

### PDB 1jjd chain A

Region: 34 - 48
Aligned: 15
Modelled: 15
Confidence: 33.3%
Identity: 47%
Fold: Metallothionein
Superfamily: Metallothionein
Family: Metallothionein

Phyre2
2 |
| c2jz3A_ |

### PDB 2jz3 chain A

Region: 10 - 16
Aligned: 7
Modelled: 7
Confidence: 29.1%
Identity: 71%
PDB header:transcription inhibitor/transcription
Chain: A: PDB Molecule:suppressor of cytokine signaling 3;
PDBTitle: socs box elonginbc ternary complex

Phyre2
3 |
| d1lv3a_ |

### PDB 1lv3 chain A

Region: 41 - 50
Aligned: 10
Modelled: 10
Confidence: 27.5%
Identity: 40%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: Hypothetical zinc finger protein YacG

Phyre2
4 |
| d1u5sb1 |

### PDB 1u5s chain B domain 1

Region: 7 - 17
Aligned: 9
Modelled: 11
Confidence: 19.9%
Identity: 33%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
5 |
| c1c94B_ |

### PDB 1c94 chain B

Region: 20 - 28
Aligned: 9
Modelled: 9
Confidence: 11.4%
Identity: 44%
PDB header:gene regulation
Chain: B: PDB Molecule:retro-gcn4 leucine zipper;
PDBTitle: reversing the sequence of the gcn4 leucine zipper does not2 affect its fold.

Phyre2
6 |
| c2w0tA_ |

### PDB 2w0t chain A

Region: 36 - 47
Aligned: 12
Modelled: 12
Confidence: 9.6%
Identity: 25%
PDB header:transcription
Chain: A: PDB Molecule:lethal(3)malignant brain tumor-like 2 protein;
PDBTitle: solution structure of the fcs zinc finger domain of human2 lmbl2

Phyre2
7 |
| c2oddA_ |

### PDB 2odd chain A

Region: 41 - 54
Aligned: 14
Modelled: 14
Confidence: 8.5%
Identity: 43%
PDB header:metal binding protein
Chain: A: PDB Molecule:protein cbfa2t1;
PDBTitle: solution structure of the mynd domain from aml1-eto2 complexed with smrt, a corepressor

Phyre2
8 |
| c1qcrD_ |

### PDB 1qcr chain D

Region: 47 - 56
Aligned: 10
Modelled: 10
Confidence: 8.3%
Identity: 30%
PDB header:
PDB COMPND:

Phyre2
9 |
| d2dj8a1 |

### PDB 2dj8 chain A domain 1

Region: 41 - 54
Aligned: 14
Modelled: 14
Confidence: 8.2%
Identity: 43%
Fold: HIT/MYND zinc finger-like
Superfamily: HIT/MYND zinc finger-like
Family: MYND zinc finger

Phyre2
10 |
| d1pg5b2 |

### PDB 1pg5 chain B domain 2

Region: 4 - 26
Aligned: 21
Modelled: 23
Confidence: 7.8%
Identity: 29%
Fold: Rubredoxin-like
Superfamily: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
Family: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain

Phyre2
11 |
| c2dj8A_ |

### PDB 2dj8 chain A

Region: 41 - 54
Aligned: 14
Modelled: 14
Confidence: 7.5%
Identity: 43%
PDB header:metal binding protein
Chain: A: PDB Molecule:protein cbfa2t1;
PDBTitle: solution structure of zf-mynd domain of protein cbfa2ti2 (protein mtg8)

Phyre2
12 |
| c3qwvA_ |

### PDB 3qwv chain A

Region: 41 - 56
Aligned: 16
Modelled: 16
Confidence: 6.7%
Identity: 38%
PDB header:transferase
Chain: A: PDB Molecule:set and mynd domain-containing protein 2;
PDBTitle: crystal structure of histone lysine methyltransferase smyd2 in complex2 with the cofactor product adohcy

Phyre2
13 |
| c2jw6A_ |

### PDB 2jw6 chain A

Region: 41 - 54
Aligned: 14
Modelled: 14
Confidence: 6.7%
Identity: 50%
PDB header:transcription
Chain: A: PDB Molecule:deformed epidermal autoregulatory factor 1 homolog;
PDBTitle: solution structure of the deaf1 mynd domain

Phyre2
14 |
| d2d8qa1 |

### PDB 2d8q chain A domain 1

Region: 41 - 54
Aligned: 14
Modelled: 14
Confidence: 6.6%
Identity: 36%
Fold: HIT/MYND zinc finger-like
Superfamily: HIT/MYND zinc finger-like
Family: MYND zinc finger

Phyre2
15 |
| d1u6pa_ |

### PDB 1u6p chain A

Region: 6 - 14
Aligned: 7
Modelled: 9
Confidence: 6.4%
Identity: 71%
Fold: Retrovirus zinc finger-like domains
Superfamily: Retrovirus zinc finger-like domains
Family: Retrovirus zinc finger-like domains

Phyre2
16 |
| c1mv4B_ |

### PDB 1mv4 chain B

Region: 12 - 18
Aligned: 7
Modelled: 7
Confidence: 6.4%
Identity: 29%
PDB header:de novo protein
Chain: B: PDB Molecule:tropomyosin 1 alpha chain;
PDBTitle: tm9a251-284: a peptide model of the c-terminus of a rat2 striated alpha tropomyosin

Phyre2
17 |
| d1ppjd1 |

### PDB 1ppj chain D domain 1

Region: 47 - 56
Aligned: 10
Modelled: 10
Confidence: 6.2%
Identity: 30%
Fold: Cytochrome c
Superfamily: Cytochrome c
Family: Cytochrome bc1 domain

Phyre2
18 |
| d2jw6a1 |

### PDB 2jw6 chain A domain 1

Region: 41 - 54
Aligned: 14
Modelled: 14
Confidence: 6.1%
Identity: 50%
Fold: HIT/MYND zinc finger-like
Superfamily: HIT/MYND zinc finger-like
Family: MYND zinc finger

Phyre2
19 |
| d1a6sa_ |

### PDB 1a6s chain A

Region: 9 - 29
Aligned: 19
Modelled: 21
Confidence: 5.9%
Identity: 37%
Fold: Retroviral matrix proteins
Superfamily: Retroviral matrix proteins
Family: GAG polyprotein M-domain

Phyre2
20 |
| c2danA_ |

### PDB 2dan chain A

Region: 41 - 54
Aligned: 14
Modelled: 14
Confidence: 5.6%
Identity: 36%
PDB header:metal binding protein
Chain: A: PDB Molecule:zinc finger mynd domain containing protein 10;
PDBTitle: the solution structure of the mynd domain (leu384-cys430)2 of human zinc finger mynd domain containing protein 10

Phyre2
21 |
22 |
23 |
24 |
25 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1jjda_ |
|  | 33.3 | 47 | Fold:Metallothionein Superfamily:Metallothionein Family:Metallothionein
2 | c2jz3A_ |
|  | 29.1 | 71 | PDB header:transcription inhibitor/transcription Chain: A: PDB Molecule:suppressor of cytokine signaling 3; PDBTitle: socs box elonginbc ternary complex
3 | d1lv3a_ |
|  | 27.5 | 40 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Hypothetical zinc finger protein YacG
4 | d1u5sb1 |
|  | 19.9 | 33 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
5 | c1c94B_ |
|  | 11.4 | 44 | PDB header:gene regulation Chain: B: PDB Molecule:retro-gcn4 leucine zipper; PDBTitle: reversing the sequence of the gcn4 leucine zipper does not2 affect its fold.
6 | c2w0tA_ |
|  | 9.6 | 25 | PDB header:transcription Chain: A: PDB Molecule:lethal(3)malignant brain tumor-like 2 protein; PDBTitle: solution structure of the fcs zinc finger domain of human2 lmbl2
7 | c2oddA_ |
|  | 8.5 | 43 | PDB header:metal binding protein Chain: A: PDB Molecule:protein cbfa2t1; PDBTitle: solution structure of the mynd domain from aml1-eto2 complexed with smrt, a corepressor
8 | c1qcrD_ |
|  | 8.3 | 30 | PDB header: PDB COMPND:
9 | d2dj8a1 |
|  | 8.2 | 43 | Fold:HIT/MYND zinc finger-like Superfamily:HIT/MYND zinc finger-like Family:MYND zinc finger
10 | d1pg5b2 |
|  | 7.8 | 29 | Fold:Rubredoxin-like Superfamily:Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain Family:Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
11 | c2dj8A_ |
|  | 7.5 | 43 | PDB header:metal binding protein Chain: A: PDB Molecule:protein cbfa2t1; PDBTitle: solution structure of zf-mynd domain of protein cbfa2ti2 (protein mtg8)
12 | c3qwvA_ |
|  | 6.7 | 38 | PDB header:transferase Chain: A: PDB Molecule:set and mynd domain-containing protein 2; PDBTitle: crystal structure of histone lysine methyltransferase smyd2 in complex2 with the cofactor product adohcy
13 | c2jw6A_ |
|  | 6.7 | 50 | PDB header:transcription Chain: A: PDB Molecule:deformed epidermal autoregulatory factor 1 homolog; PDBTitle: solution structure of the deaf1 mynd domain
14 | d2d8qa1 |
|  | 6.6 | 36 | Fold:HIT/MYND zinc finger-like Superfamily:HIT/MYND zinc finger-like Family:MYND zinc finger
15 | d1u6pa_ |
|  | 6.4 | 71 | Fold:Retrovirus zinc finger-like domains Superfamily:Retrovirus zinc finger-like domains Family:Retrovirus zinc finger-like domains
16 | c1mv4B_ |
|  | 6.4 | 29 | PDB header:de novo protein Chain: B: PDB Molecule:tropomyosin 1 alpha chain; PDBTitle: tm9a251-284: a peptide model of the c-terminus of a rat2 striated alpha tropomyosin
17 | d1ppjd1 |
|  | 6.2 | 30 | Fold:Cytochrome c Superfamily:Cytochrome c Family:Cytochrome bc1 domain
18 | d2jw6a1 |
|  | 6.1 | 50 | Fold:HIT/MYND zinc finger-like Superfamily:HIT/MYND zinc finger-like Family:MYND zinc finger
19 | d1a6sa_ |
|  | 5.9 | 37 | Fold:Retroviral matrix proteins Superfamily:Retroviral matrix proteins Family:GAG polyprotein M-domain
20 | c2danA_ |
|  | 5.6 | 36 | PDB header:metal binding protein Chain: A: PDB Molecule:zinc finger mynd domain containing protein 10; PDBTitle: the solution structure of the mynd domain (leu384-cys430)2 of human zinc finger mynd domain containing protein 10
21 | c3iz5w_ |
| not modelled | 5.6 | 21 | PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l22 (l22e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
22 | c2yiuE_ |
| not modelled | 5.6 | 50 | PDB header:oxidoreductase Chain: E: PDB Molecule:cytochrome c1, heme protein; PDBTitle: x-ray structure of the dimeric cytochrome bc1 complex from2 the soil bacterium paracoccus denitrificans at 2.73 angstrom resolution
23 | d1ubdc2 |
| not modelled | 5.5 | 44 | Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2
24 | d2dana1 |
| not modelled | 5.5 | 36 | Fold:HIT/MYND zinc finger-like Superfamily:HIT/MYND zinc finger-like Family:MYND zinc finger
25 | d3cx5d1 |
| not modelled | 5.4 | 40 | Fold:Cytochrome c Superfamily:Cytochrome c Family:Cytochrome bc1 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