Phyre 2 Results for P64604

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Email | l.a.kelley@imperial.ac.uk
Description | P64604
Date | Thu Jan 5 12:09:51 GMT 2012
Unique Job ID | 072527d03382ef2e

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1v5va1
Top template information
Fold:Elongation factor/aminomethyltransferase common domain Superfamily:Aminomethyltransferase beta-barrel domain Family:Aminomethyltransferase beta-barrel domain
Confidence and coverage
Confidence: | 64.8% | Coverage: | 33%
61 residues ( 33% of your sequence) have been modelled with 64.8% 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.
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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 | Q | T | K | K | N | E | I | W | V | G | I | F | L | L | A | A | L | L | A | A | L | F | V | C | L | K | A | A | N | V | T | S | I | R | T | E | P | T | Y | T | L | Y | A | T | F | D | N | I | G | G | L | K | A | R | S | P | V | S | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | G | G | V | V | V | G | R | V | A | D | I | T | L | D | P | K | T | Y | L | P | R | V | T | L | E | I | E | Q | R | Y | N | H | I | P | D | T | S | S | L | S | I | R | T | S | G | L | L | G | E | Q | Y | L | A | L | N | V | G | F | E | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? | ? |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | P | E | L | G | T | A | I | L | K | D | G | D | T | I | Q | D | T | K | S | A | M | V | L | E | D | L | I | G | Q | F | L | Y | G | S | K | G | D | D | N | K | N | S | G | D | A | P | A | A | A | P | G | N | N | E | T | T | E | P | V | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? |  | ? |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | .
Sequence |  | T | T | 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 |
| d1v5va1 |

### PDB 1v5v chain A domain 1

Region: 41 - 101
Aligned: 61
Modelled: 61
Confidence: 64.8%
Identity: 16%
Fold: Elongation factor/aminomethyltransferase common domain
Superfamily: Aminomethyltransferase beta-barrel domain
Family: Aminomethyltransferase beta-barrel domain

Phyre2
2 |
| c2j5uB_ |

### PDB 2j5u chain B

Region: 61 - 93
Aligned: 33
Modelled: 33
Confidence: 63.6%
Identity: 9%
PDB header:cell shape regulation
Chain: B: PDB Molecule:mrec protein;
PDBTitle: mrec lysteria monocytogenes

Phyre2
3 |
| c1v5vA_ |

### PDB 1v5v chain A

Region: 38 - 105
Aligned: 66
Modelled: 68
Confidence: 40.2%
Identity: 15%
PDB header:transferase
Chain: A: PDB Molecule:aminomethyltransferase;
PDBTitle: crystal structure of a component of glycine cleavage system: t-protein2 from pyrococcus horikoshii ot3 at 1.5 a resolution

Phyre2
4 |
| c2qf4A_ |

### PDB 2qf4 chain A

Region: 41 - 108
Aligned: 63
Modelled: 68
Confidence: 32.2%
Identity: 14%
PDB header:structural protein
Chain: A: PDB Molecule:cell shape determining protein mrec;
PDBTitle: high resolution structure of the major periplasmic domain from the2 cell shape-determining filament mrec (orthorhombic form)

Phyre2
5 |
| d1pj5a1 |

### PDB 1pj5 chain A domain 1

Region: 42 - 101
Aligned: 59
Modelled: 60
Confidence: 15.2%
Identity: 17%
Fold: Elongation factor/aminomethyltransferase common domain
Superfamily: Aminomethyltransferase beta-barrel domain
Family: Aminomethyltransferase beta-barrel domain

Phyre2
6 |
| d1wosa1 |

### PDB 1wos chain A domain 1

Region: 41 - 105
Aligned: 63
Modelled: 65
Confidence: 13.9%
Identity: 10%
Fold: Elongation factor/aminomethyltransferase common domain
Superfamily: Aminomethyltransferase beta-barrel domain
Family: Aminomethyltransferase beta-barrel domain

Phyre2
7 |
| c1yx2B_ |

### PDB 1yx2 chain B

Region: 36 - 101
Aligned: 66
Modelled: 66
Confidence: 12.9%
Identity: 17%
PDB header:transferase
Chain: B: PDB Molecule:aminomethyltransferase;
PDBTitle: crystal structure of the probable aminomethyltransferase2 from bacillus subtilis

Phyre2
8 |
| c1cz5A_ |

### PDB 1cz5 chain A

Region: 51 - 116
Aligned: 65
Modelled: 66
Confidence: 11.0%
Identity: 11%
PDB header:hydrolase
Chain: A: PDB Molecule:vcp-like atpase;
PDBTitle: nmr structure of vat-n: the n-terminal domain of vat (vcp-2 like atpase of thermoplasma)

Phyre2
9 |
| c2k6zA_ |

### PDB 2k6z chain A

Region: 25 - 61
Aligned: 37
Modelled: 37
Confidence: 10.5%
Identity: 16%
PDB header:metal transport
Chain: A: PDB Molecule:putative uncharacterized protein ttha1943;
PDBTitle: solution structures of copper loaded form pcua (trans2 conformation of the peptide bond involving the nitrogen of3 p14)

Phyre2
10 |
| d1h9ra2 |

### PDB 1h9r chain A domain 2

Region: 66 - 108
Aligned: 36
Modelled: 43
Confidence: 9.2%
Identity: 8%
Fold: OB-fold
Superfamily: MOP-like
Family: BiMOP, duplicated molybdate-binding domain

Phyre2
11 |
| d1x9la_ |

### PDB 1x9l chain A

Region: 25 - 59
Aligned: 35
Modelled: 35
Confidence: 8.1%
Identity: 9%
Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily: DR1885-like metal-binding protein
Family: DR1885-like metal-binding protein

Phyre2
12 |
| c3htrB_ |

### PDB 3htr chain B

Region: 54 - 81
Aligned: 28
Modelled: 28
Confidence: 7.9%
Identity: 11%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized prc-barrel domain protein;
PDBTitle: crystal structure of prc-barrel domain protein from2 rhodopseudomonas palustris

Phyre2
13 |
| c1t5eB_ |

### PDB 1t5e chain B

Region: 35 - 61
Aligned: 27
Modelled: 27
Confidence: 7.8%
Identity: 22%
PDB header:transport protein
Chain: B: PDB Molecule:multidrug resistance protein mexa;
PDBTitle: the structure of mexa

Phyre2
14 |
| d1nnxa_ |

### PDB 1nnx chain A

Region: 48 - 102
Aligned: 55
Modelled: 55
Confidence: 7.5%
Identity: 16%
Fold: OB-fold
Superfamily: Hypothetical protein YgiW
Family: Hypothetical protein YgiW

Phyre2
15 |
| d1vf7a_ |

### PDB 1vf7 chain A

Region: 35 - 61
Aligned: 27
Modelled: 27
Confidence: 7.3%
Identity: 22%
Fold: HlyD-like secretion proteins
Superfamily: HlyD-like secretion proteins
Family: HlyD-like secretion proteins

Phyre2
16 |
| d2cp6a1 |

### PDB 2cp6 chain A domain 1

Region: 50 - 90
Aligned: 41
Modelled: 41
Confidence: 6.9%
Identity: 20%
Fold: SH3-like barrel
Superfamily: Cap-Gly domain
Family: Cap-Gly domain

Phyre2
17 |
| d1gtra1 |

### PDB 1gtr chain A domain 1

Region: 41 - 89
Aligned: 49
Modelled: 49
Confidence: 6.8%
Identity: 8%
Fold: Ribosomal protein L25-like
Superfamily: Ribosomal protein L25-like
Family: Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain

Phyre2
18 |
| d2vv5a1 |

### PDB 2vv5 chain A domain 1

Region: 52 - 73
Aligned: 21
Modelled: 22
Confidence: 6.5%
Identity: 33%
Fold: Sm-like fold
Superfamily: Sm-like ribonucleoproteins
Family: Mechanosensitive channel protein MscS (YggB), middle domain

Phyre2

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1v5va1 |
|  | 64.8 | 16 | Fold:Elongation factor/aminomethyltransferase common domain Superfamily:Aminomethyltransferase beta-barrel domain Family:Aminomethyltransferase beta-barrel domain
2 | c2j5uB_ |
|  | 63.6 | 9 | PDB header:cell shape regulation Chain: B: PDB Molecule:mrec protein; PDBTitle: mrec lysteria monocytogenes
3 | c1v5vA_ |
|  | 40.2 | 15 | PDB header:transferase Chain: A: PDB Molecule:aminomethyltransferase; PDBTitle: crystal structure of a component of glycine cleavage system: t-protein2 from pyrococcus horikoshii ot3 at 1.5 a resolution
4 | c2qf4A_ |
|  | 32.2 | 14 | PDB header:structural protein Chain: A: PDB Molecule:cell shape determining protein mrec; PDBTitle: high resolution structure of the major periplasmic domain from the2 cell shape-determining filament mrec (orthorhombic form)
5 | d1pj5a1 |
|  | 15.2 | 17 | Fold:Elongation factor/aminomethyltransferase common domain Superfamily:Aminomethyltransferase beta-barrel domain Family:Aminomethyltransferase beta-barrel domain
6 | d1wosa1 |
|  | 13.9 | 10 | Fold:Elongation factor/aminomethyltransferase common domain Superfamily:Aminomethyltransferase beta-barrel domain Family:Aminomethyltransferase beta-barrel domain
7 | c1yx2B_ |
|  | 12.9 | 17 | PDB header:transferase Chain: B: PDB Molecule:aminomethyltransferase; PDBTitle: crystal structure of the probable aminomethyltransferase2 from bacillus subtilis
8 | c1cz5A_ |
|  | 11.0 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:vcp-like atpase; PDBTitle: nmr structure of vat-n: the n-terminal domain of vat (vcp-2 like atpase of thermoplasma)
9 | c2k6zA_ |
|  | 10.5 | 16 | PDB header:metal transport Chain: A: PDB Molecule:putative uncharacterized protein ttha1943; PDBTitle: solution structures of copper loaded form pcua (trans2 conformation of the peptide bond involving the nitrogen of3 p14)
10 | d1h9ra2 |
|  | 9.2 | 8 | Fold:OB-fold Superfamily:MOP-like Family:BiMOP, duplicated molybdate-binding domain
11 | d1x9la_ |
|  | 8.1 | 9 | Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:DR1885-like metal-binding protein Family:DR1885-like metal-binding protein
12 | c3htrB_ |
|  | 7.9 | 11 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized prc-barrel domain protein; PDBTitle: crystal structure of prc-barrel domain protein from2 rhodopseudomonas palustris
13 | c1t5eB_ |
|  | 7.8 | 22 | PDB header:transport protein Chain: B: PDB Molecule:multidrug resistance protein mexa; PDBTitle: the structure of mexa
14 | d1nnxa_ |
|  | 7.5 | 16 | Fold:OB-fold Superfamily:Hypothetical protein YgiW Family:Hypothetical protein YgiW
15 | d1vf7a_ |
|  | 7.3 | 22 | Fold:HlyD-like secretion proteins Superfamily:HlyD-like secretion proteins Family:HlyD-like secretion proteins
16 | d2cp6a1 |
|  | 6.9 | 20 | Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain
17 | d1gtra1 |
|  | 6.8 | 8 | Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain
18 | d2vv5a1 |
|  | 6.5 | 33 | Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Mechanosensitive channel protein MscS (YggB), middle 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

Transmembrane helix prediction |

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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