Phyre 2 Results for P21515

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Email | l.a.kelley@imperial.ac.uk
Description | P21515
Date | Thu Jan 5 11:38:26 GMT 2012
Unique Job ID | 0a724e62aee86cb7

Summary |

Top model
Image coloured by rainbow N → C terminus
| Close Jmol

Model (left) based on template d1riqa1
Top template information
Fold:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Superfamily:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Family:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
Confidence and coverage
Confidence: | 27.5% | Coverage: | 40%
78 residues ( 40% of your sequence) have been modelled with 27.5% 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 | N | F | L | A | H | L | H | L | A | H | L | A | E | S | S | L | S | G | N | L | L | A | D | F | V | R | G | N | P | E | E | S | F | P | P | D | V | V | A | G | I | H | M | H | R | R | I | D | V | L | T | D | N | L | P | E | V | R | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | A | R | E | W | F | R | S | E | T | R | R | V | A | P | I | T | L | D | V | M | W | D | H | F | L | S | R | H | W | S | Q | L | S | P | D | F | P | L | Q | E | F | V | C | Y | A | R | E | Q | V | M | T | I | L | P | D | S | P | P | R | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | I | N | L | N | N | Y | L | W | S | E | Q | W | L | V | R | Y | R | D | M | D | F | I | Q | N | V | L | N | G | M | A | S | R | R | P | R | L | D | A | L | R | D | S | W | Y | D | L | D | A | H | Y | D | A | L | E | T | R | F | W | Q | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | .
Sequence |  | Y | P | R | M | M | A | Q | A | S | R | K | A | 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 |
| d1riqa1 |

### PDB 1riq chain A domain 1

Region: 102 - 190
Aligned: 78
Modelled: 89
Confidence: 27.5%
Identity: 13%
Fold: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
Superfamily: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
Family: Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)

Phyre2
2 |
| d1s5qb_ |

### PDB 1s5q chain B

Region: 102 - 183
Aligned: 76
Modelled: 82
Confidence: 23.8%
Identity: 13%
Fold: PAH2 domain
Superfamily: PAH2 domain
Family: PAH2 domain

Phyre2
3 |
| d1x1na1 |

### PDB 1x1n chain A domain 1

Region: 99 - 193
Aligned: 95
Modelled: 95
Confidence: 16.1%
Identity: 15%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: Amylase, catalytic domain

Phyre2
4 |
| d1r7ma1 |

### PDB 1r7m chain A domain 1

Region: 15 - 24
Aligned: 10
Modelled: 10
Confidence: 13.5%
Identity: 30%
Fold: Homing endonuclease-like
Superfamily: Homing endonucleases
Family: Group I mobile intron endonuclease

Phyre2
5 |
| d1icha_ |

### PDB 1ich chain A

Region: 74 - 152
Aligned: 76
Modelled: 79
Confidence: 12.6%
Identity: 12%
Fold: DEATH domain
Superfamily: DEATH domain
Family: DEATH domain, DD

Phyre2
6 |
| c1ichA_ |

### PDB 1ich chain A

Region: 74 - 152
Aligned: 76
Modelled: 79
Confidence: 12.6%
Identity: 12%
PDB header:apoptosis
Chain: A: PDB Molecule:tumor necrosis factor receptor-1;
PDBTitle: solution structure of the tumor necrosis factor receptor-12 death domain

Phyre2
7 |
| d1puza_ |

### PDB 1puz chain A

Region: 77 - 129
Aligned: 52
Modelled: 53
Confidence: 10.7%
Identity: 17%
Fold: YgfY-like
Superfamily: YgfY-like
Family: YgfY-like

Phyre2
8 |
| c1yfsB_ |

### PDB 1yfs chain B

Region: 140 - 190
Aligned: 51
Modelled: 51
Confidence: 10.6%
Identity: 14%
PDB header:ligase
Chain: B: PDB Molecule:alanyl-trna synthetase;
PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine

Phyre2
9 |
| d1vhba_ |

### PDB 1vhb chain A

Region: 85 - 185
Aligned: 92
Modelled: 101
Confidence: 8.9%
Identity: 10%
Fold: Globin-like
Superfamily: Globin-like
Family: Globins

Phyre2
10 |
| c2jr5A_ |

### PDB 2jr5 chain A

Region: 77 - 131
Aligned: 54
Modelled: 55
Confidence: 8.9%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0350 protein vc_2471;
PDBTitle: solution structure of upf0350 protein vc_2471. northeast2 structural genomics target vcr36

Phyre2
11 |
| c3hxxA_ |

### PDB 3hxx chain A

Region: 140 - 186
Aligned: 47
Modelled: 47
Confidence: 8.2%
Identity: 11%
PDB header:ligase
Chain: A: PDB Molecule:alanyl-trna synthetase;
PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp

Phyre2
12 |
| c1x6iB_ |

### PDB 1x6i chain B

Region: 77 - 131
Aligned: 54
Modelled: 55
Confidence: 7.9%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein ygfy;
PDBTitle: crystal structure of ygfy from escherichia coli

Phyre2
13 |
| d1yh2a1 |

### PDB 1yh2 chain A domain 1

Region: 129 - 191
Aligned: 59
Modelled: 63
Confidence: 7.7%
Identity: 15%
Fold: UBC-like
Superfamily: UBC-like
Family: UBC-related

Phyre2
14 |
| d1muka_ |

### PDB 1muk chain A

Region: 52 - 93
Aligned: 40
Modelled: 42
Confidence: 7.4%
Identity: 28%
Fold: DNA/RNA polymerases
Superfamily: DNA/RNA polymerases
Family: RNA-dependent RNA-polymerase

Phyre2
15 |
| d2f05a1 |

### PDB 2f05 chain A domain 1

Region: 156 - 183
Aligned: 28
Modelled: 28
Confidence: 7.2%
Identity: 21%
Fold: PAH2 domain
Superfamily: PAH2 domain
Family: PAH2 domain

Phyre2
16 |
| c1r7mA_ |

### PDB 1r7m chain A

Region: 9 - 24
Aligned: 16
Modelled: 16
Confidence: 6.6%
Identity: 25%
PDB header:hydrolase/dna
Chain: A: PDB Molecule:intron-encoded endonuclease i-scei;
PDBTitle: the homing endonuclease i-scei bound to its dna recognition2 region

Phyre2
17 |
| d2a0ba_ |

### PDB 2a0b chain A

Region: 103 - 192
Aligned: 86
Modelled: 90
Confidence: 6.5%
Identity: 8%
Fold: Four-helical up-and-down bundle
Superfamily: Histidine-containing phosphotransfer domain, HPT domain
Family: Aerobic respiration control sensor protein, ArcB

Phyre2
18 |
| d1fada_ |

### PDB 1fad chain A

Region: 76 - 152
Aligned: 72
Modelled: 77
Confidence: 6.4%
Identity: 11%
Fold: DEATH domain
Superfamily: DEATH domain
Family: DEATH domain, DD

Phyre2
19 |
| c2jynA_ |

### PDB 2jyn chain A

Region: 166 - 184
Aligned: 19
Modelled: 19
Confidence: 6.0%
Identity: 21%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0368 protein ypl225w;
PDBTitle: a novel solution nmr structure of protein yst0336 from2 saccharomyces cerevisiae. northeast structural genomics3 consortium target yt51/ontario centre for structural4 proteomics target yst0336

Phyre2
20 |
| c4a56A_ |

### PDB 4a56 chain A

Region: 86 - 128
Aligned: 42
Modelled: 43
Confidence: 5.9%
Identity: 14%
PDB header:protein transport
Chain: A: PDB Molecule:pullulanase secretion protein puls;
PDBTitle: crystal structure of the type 2 secretion system pilotin2 from klebsiella oxytoca

Phyre2
21 |
22 |
23 |
24 |
25 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1riqa1 |
|  | 27.5 | 13 | Fold:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Superfamily:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Family:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
2 | d1s5qb_ |
|  | 23.8 | 13 | Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain
3 | d1x1na1 |
|  | 16.1 | 15 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
4 | d1r7ma1 |
|  | 13.5 | 30 | Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Group I mobile intron endonuclease
5 | d1icha_ |
|  | 12.6 | 12 | Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD
6 | c1ichA_ |
|  | 12.6 | 12 | PDB header:apoptosis Chain: A: PDB Molecule:tumor necrosis factor receptor-1; PDBTitle: solution structure of the tumor necrosis factor receptor-12 death domain
7 | d1puza_ |
|  | 10.7 | 17 | Fold:YgfY-like Superfamily:YgfY-like Family:YgfY-like
8 | c1yfsB_ |
|  | 10.6 | 14 | PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine
9 | d1vhba_ |
|  | 8.9 | 10 | Fold:Globin-like Superfamily:Globin-like Family:Globins
10 | c2jr5A_ |
|  | 8.9 | 17 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0350 protein vc_2471; PDBTitle: solution structure of upf0350 protein vc_2471. northeast2 structural genomics target vcr36
11 | c3hxxA_ |
|  | 8.2 | 11 | PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp
12 | c1x6iB_ |
|  | 7.9 | 17 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ygfy; PDBTitle: crystal structure of ygfy from escherichia coli
13 | d1yh2a1 |
|  | 7.7 | 15 | Fold:UBC-like Superfamily:UBC-like Family:UBC-related
14 | d1muka_ |
|  | 7.4 | 28 | Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase
15 | d2f05a1 |
|  | 7.2 | 21 | Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain
16 | c1r7mA_ |
|  | 6.6 | 25 | PDB header:hydrolase/dna Chain: A: PDB Molecule:intron-encoded endonuclease i-scei; PDBTitle: the homing endonuclease i-scei bound to its dna recognition2 region
17 | d2a0ba_ |
|  | 6.5 | 8 | Fold:Four-helical up-and-down bundle Superfamily:Histidine-containing phosphotransfer domain, HPT domain Family:Aerobic respiration control sensor protein, ArcB
18 | d1fada_ |
|  | 6.4 | 11 | Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD
19 | c2jynA_ |
|  | 6.0 | 21 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0368 protein ypl225w; PDBTitle: a novel solution nmr structure of protein yst0336 from2 saccharomyces cerevisiae. northeast structural genomics3 consortium target yt51/ontario centre for structural4 proteomics target yst0336
20 | c4a56A_ |
|  | 5.9 | 14 | PDB header:protein transport Chain: A: PDB Molecule:pullulanase secretion protein puls; PDBTitle: crystal structure of the type 2 secretion system pilotin2 from klebsiella oxytoca
21 | d1rg6a_ |
| not modelled | 5.6 | 24 | Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain
22 | c2yqfA_ |
| not modelled | 5.3 | 13 | PDB header:protein binding Chain: A: PDB Molecule:ankyrin-1; PDBTitle: solution structure of the death domain of ankyrin-1
23 | c1ztaA_ |
| not modelled | 5.2 | 26 | PDB header:dna-binding motif Chain: A: PDB Molecule:leucine zipper monomer; PDBTitle: the solution structure of a leucine-zipper motif peptide
24 | d2incc1 |
| not modelled | 5.2 | 40 | Fold:beta-Grasp (ubiquitin-like) Superfamily:TmoB-like Family:TmoB-like
25 | d1svda2 |
| not modelled | 5.1 | 42 | Fold:Ferredoxin-like Superfamily:RuBisCO, large subunit, small (N-terminal) domain Family:Ribulose 1,5-bisphosphate carboxylase-oxygenase

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
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