Phyre 2 Results for P0A6G3

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P0A6G3
Date | Thu Jan 5 11:03:05 GMT 2012
Unique Job ID | 5f73ed93e5dd5bc4

Summary |

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

Model (left) based on template d2a9sa1
Top template information
Fold:Anticodon-binding domain-like Superfamily:CinA-like Family:CinA-like
Confidence and coverage
Confidence: | 100.0% | Coverage: | 97%
160 residues ( 97% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | T | D | S | E | L | M | Q | L | S | E | Q | V | G | Q | A | L | K | A | R | G | A | T | V | T | T | A | E | S | C | T | G | G | W | V | A | K | V | I | T | D | I | A | G | S | S | A | W | F | E | R | G | F | V | T | Y | S | N | E | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | K | A | Q | M | I | G | V | R | E | E | T | L | A | Q | H | G | A | V | S | E | P | V | V | V | E | M | A | I | G | A | L | K | A | A | R | A | D | Y | A | V | S | I | S | G | I | A | G | P | D | G | G | S | E | E | K | P | V | G | T | V
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? | ? | ? | ? |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | .
Sequence |  | W | F | A | F | A | T | A | R | G | E | G | I | T | R | R | E | C | F | S | G | D | R | D | A | V | R | R | Q | A | T | A | Y | A | L | Q | T | L | W | Q | Q | F | L | Q | N | T
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 |
| d2a9sa1 |

### PDB 2a9s chain A domain 1

Region: 4 - 163
Aligned: 160
Modelled: 160
Confidence: 100.0%
Identity: 43%
Fold: Anticodon-binding domain-like
Superfamily: CinA-like
Family: CinA-like

Phyre2
2 |
| d1pzna1 |

### PDB 1pzn chain A domain 1

Region: 39 - 95
Aligned: 57
Modelled: 57
Confidence: 51.6%
Identity: 18%
Fold: SAM domain-like
Superfamily: Rad51 N-terminal domain-like
Family: DNA repair protein Rad51, N-terminal domain

Phyre2
3 |
| d2i1qa1 |

### PDB 2i1q chain A domain 1

Region: 39 - 95
Aligned: 57
Modelled: 57
Confidence: 42.3%
Identity: 18%
Fold: SAM domain-like
Superfamily: Rad51 N-terminal domain-like
Family: DNA repair protein Rad51, N-terminal domain

Phyre2
4 |
| c3b33A_ |

### PDB 3b33 chain A

Region: 34 - 72
Aligned: 39
Modelled: 39
Confidence: 38.6%
Identity: 8%
PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus

Phyre2
5 |
| c3a9lB_ |

### PDB 3a9l chain B

Region: 35 - 123
Aligned: 66
Modelled: 89
Confidence: 36.5%
Identity: 23%
PDB header:hydrolase
Chain: B: PDB Molecule:poly-gamma-glutamate hydrolase;
PDBTitle: structure of bacteriophage poly-gamma-glutamate hydrolase

Phyre2
6 |
| d1mzua_ |

### PDB 1mzu chain A

Region: 52 - 72
Aligned: 21
Modelled: 21
Confidence: 18.1%
Identity: 19%
Fold: Profilin-like
Superfamily: PYP-like sensor domain (PAS domain)
Family: PYP-like

Phyre2
7 |
| d1xjca_ |

### PDB 1xjc chain A

Region: 7 - 27
Aligned: 21
Modelled: 21
Confidence: 17.0%
Identity: 29%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Nitrogenase iron protein-like

Phyre2
8 |
| d1v9ya_ |

### PDB 1v9y chain A

Region: 33 - 72
Aligned: 40
Modelled: 40
Confidence: 17.0%
Identity: 18%
Fold: Profilin-like
Superfamily: PYP-like sensor domain (PAS domain)
Family: Heme-binding PAS domain

Phyre2
9 |
| c1v9yA_ |

### PDB 1v9y chain A

Region: 33 - 72
Aligned: 40
Modelled: 40
Confidence: 17.0%
Identity: 18%
PDB header:signaling protein
Chain: A: PDB Molecule:heme pas sensor protein;
PDBTitle: crystal structure of the heme pas sensor domain of ec dos (ferric2 form)

Phyre2
10 |
| c3mfxA_ |

### PDB 3mfx chain A

Region: 34 - 72
Aligned: 39
Modelled: 39
Confidence: 15.9%
Identity: 15%
PDB header:transcription
Chain: A: PDB Molecule:sensory box/ggdef family protein;
PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b

Phyre2
11 |
| d2bgwa1 |

### PDB 2bgw chain A domain 1

Region: 37 - 95
Aligned: 58
Modelled: 59
Confidence: 13.6%
Identity: 5%
Fold: SAM domain-like
Superfamily: RuvA domain 2-like
Family: Hef domain-like

Phyre2
12 |
| c3ju7B_ |

### PDB 3ju7 chain B

Region: 5 - 108
Aligned: 104
Modelled: 104
Confidence: 13.1%
Identity: 11%
PDB header:transferase
Chain: B: PDB Molecule:putative plp-dependent aminotransferase;
PDBTitle: crystal structure of putative plp-dependent aminotransferase2 (np_978343.1) from bacillus cereus atcc 10987 at 2.19 a resolution

Phyre2
13 |
| d3proc1 |

### PDB 3pro chain C domain 1

Region: 60 - 99
Aligned: 38
Modelled: 40
Confidence: 11.8%
Identity: 18%
Fold: Alpha-lytic protease prodomain-like
Superfamily: Alpha-lytic protease prodomain
Family: Alpha-lytic protease prodomain

Phyre2
14 |
| c1zpdA_ |

### PDB 1zpd chain A

Region: 8 - 104
Aligned: 71
Modelled: 73
Confidence: 11.0%
Identity: 17%
PDB header:alcohol fermentation
Chain: A: PDB Molecule:pyruvate decarboxylase;
PDBTitle: pyruvate decarboxylase from zymomonas mobilis

Phyre2
15 |
| d1nwza_ |

### PDB 1nwz chain A

Region: 52 - 72
Aligned: 21
Modelled: 21
Confidence: 10.7%
Identity: 19%
Fold: Profilin-like
Superfamily: PYP-like sensor domain (PAS domain)
Family: PYP-like

Phyre2
16 |
| c1kftA_ |

### PDB 1kft chain A

Region: 36 - 92
Aligned: 56
Modelled: 57
Confidence: 10.6%
Identity: 11%
PDB header:dna binding protein
Chain: A: PDB Molecule:excinuclease abc subunit c;
PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli

Phyre2
17 |
| d1kfta_ |

### PDB 1kft chain A

Region: 36 - 92
Aligned: 56
Modelled: 57
Confidence: 10.6%
Identity: 11%
Fold: SAM domain-like
Superfamily: RuvA domain 2-like
Family: Excinuclease UvrC C-terminal domain

Phyre2
18 |
| d1a4ia1 |

### PDB 1a4i chain A domain 1

Region: 13 - 127
Aligned: 59
Modelled: 60
Confidence: 10.3%
Identity: 36%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Aminoacid dehydrogenase-like, C-terminal domain

Phyre2
19 |
| c3a0vA_ |

### PDB 3a0v chain A

Region: 52 - 72
Aligned: 21
Modelled: 21
Confidence: 10.2%
Identity: 29%
PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m)

Phyre2
20 |
| c2w1tB_ |

### PDB 2w1t chain B

Region: 72 - 103
Aligned: 30
Modelled: 32
Confidence: 9.7%
Identity: 23%
PDB header:transcription
Chain: B: PDB Molecule:stage v sporulation protein t;
PDBTitle: crystal structure of b. subtilis spovt

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2a9sa1 |
|  | 100.0 | 43 | Fold:Anticodon-binding domain-like Superfamily:CinA-like Family:CinA-like
2 | d1pzna1 |
|  | 51.6 | 18 | Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain
3 | d2i1qa1 |
|  | 42.3 | 18 | Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain
4 | c3b33A_ |
|  | 38.6 | 8 | PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus
5 | c3a9lB_ |
|  | 36.5 | 23 | PDB header:hydrolase Chain: B: PDB Molecule:poly-gamma-glutamate hydrolase; PDBTitle: structure of bacteriophage poly-gamma-glutamate hydrolase
6 | d1mzua_ |
|  | 18.1 | 19 | Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like
7 | d1xjca_ |
|  | 17.0 | 29 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
8 | d1v9ya_ |
|  | 17.0 | 18 | Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Heme-binding PAS domain
9 | c1v9yA_ |
|  | 17.0 | 18 | PDB header:signaling protein Chain: A: PDB Molecule:heme pas sensor protein; PDBTitle: crystal structure of the heme pas sensor domain of ec dos (ferric2 form)
10 | c3mfxA_ |
|  | 15.9 | 15 | PDB header:transcription Chain: A: PDB Molecule:sensory box/ggdef family protein; PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b
11 | d2bgwa1 |
|  | 13.6 | 5 | Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like
12 | c3ju7B_ |
|  | 13.1 | 11 | PDB header:transferase Chain: B: PDB Molecule:putative plp-dependent aminotransferase; PDBTitle: crystal structure of putative plp-dependent aminotransferase2 (np_978343.1) from bacillus cereus atcc 10987 at 2.19 a resolution
13 | d3proc1 |
|  | 11.8 | 18 | Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain
14 | c1zpdA_ |
|  | 11.0 | 17 | PDB header:alcohol fermentation Chain: A: PDB Molecule:pyruvate decarboxylase; PDBTitle: pyruvate decarboxylase from zymomonas mobilis
15 | d1nwza_ |
|  | 10.7 | 19 | Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like
16 | c1kftA_ |
|  | 10.6 | 11 | PDB header:dna binding protein Chain: A: PDB Molecule:excinuclease abc subunit c; PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli
17 | d1kfta_ |
|  | 10.6 | 11 | Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Excinuclease UvrC C-terminal domain
18 | d1a4ia1 |
|  | 10.3 | 36 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain
19 | c3a0vA_ |
|  | 10.2 | 29 | PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m)
20 | c2w1tB_ |
|  | 9.7 | 23 | PDB header:transcription Chain: B: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of b. subtilis spovt
21 | d1j3ma_ |
| not modelled | 9.6 | 9 | Fold:TBP-like Superfamily:TT1751-like Family:TT1751-like
22 | c3mqoB_ |
| not modelled | 9.6 | 8 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: the crystal structure of the pas domain in complex with isopropanol of2 a transcriptional regulator in the luxr family from burkholderia3 thailandensis to 1.7a
23 | c3fg8B_ |
| not modelled | 9.5 | 14 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein rha05790; PDBTitle: crystal structure of pas domain of rha05790
24 | c2v3wC_ |
| not modelled | 8.6 | 22 | PDB header:lyase Chain: C: PDB Molecule:benzoylformate decarboxylase; PDBTitle: crystal structure of the benzoylformate decarboxylase2 variant l461a from pseudomonas putida
25 | c2v1bA_ |
| not modelled | 8.3 | 10 | PDB header:transferase Chain: A: PDB Molecule:nph1-1; PDBTitle: n- and c-terminal helices of oat lov2 (404-546) are2 involved in light-induced signal transduction (room3 temperature (293k) light structure of lov2 (404-546))
26 | c3p7nB_ |
| not modelled | 8.0 | 26 | PDB header:dna binding protein Chain: B: PDB Molecule:sensor histidine kinase; PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis
27 | d1otda_ |
| not modelled | 7.2 | 17 | Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like
28 | c2xc7A_ |
| not modelled | 7.2 | 10 | PDB header:rna binding protein Chain: A: PDB Molecule:phosphorylated adapter rna export protein; PDBTitle: solution structure of phax-rbd in complex with ssrna
29 | d1s2da_ |
| not modelled | 6.5 | 14 | Fold:Flavodoxin-like Superfamily:N-(deoxy)ribosyltransferase-like Family:N-deoxyribosyltransferase
30 | d2a1jb1 |
| not modelled | 6.3 | 13 | Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like
31 | d1rqpa2 |
| not modelled | 6.2 | 31 | Fold:Bacterial fluorinating enzyme, N-terminal domain Superfamily:Bacterial fluorinating enzyme, N-terminal domain Family:Bacterial fluorinating enzyme, N-terminal domain
32 | c1wu8B_ |
| not modelled | 6.1 | 31 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0463; PDBTitle: crystal structure of project ph0463 from pyrococcus horikoshii ot3
33 | c3rtyA_ |
| not modelled | 6.0 | 19 | PDB header:circadian clock protein Chain: A: PDB Molecule:period circadian protein; PDBTitle: structure of an enclosed dimer formed by the drosophila period protein
34 | d2ge7a1 |
| not modelled | 6.0 | 23 | Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Coronavirus nucleocapsid protein
35 | d2ca1a1 |
| not modelled | 5.9 | 23 | Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Coronavirus nucleocapsid protein
36 | c2npbA_ |
| not modelled | 5.8 | 14 | PDB header:oxidoreductase Chain: A: PDB Molecule:selenoprotein w; PDBTitle: nmr solution structure of mouse selw
37 | d1ciia1 |
| not modelled | 5.8 | 30 | Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin
38 | c2zbvC_ |
| not modelled | 5.8 | 23 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of uncharacterized conserved protein from thermotoga2 maritima
39 | c2e62A_ |
| not modelled | 5.8 | 25 | PDB header:rna binding protein Chain: A: PDB Molecule:protein at5g25060; PDBTitle: solution structure of the cwf21 domain in protein aak25922
40 | c2guzO_ |
| not modelled | 5.7 | 16 | PDB header:chaperone, protein transport Chain: O: PDB Molecule:mitochondrial import inner membrane translocase PDBTitle: structure of the tim14-tim16 complex of the mitochondrial2 protein import motor
41 | c3gdwA_ |
| not modelled | 5.6 | 9 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:sigma-54 interaction domain protein; PDBTitle: crystal structure of sigma-54 interaction domain protein from2 enterococcus faecalis
42 | d1e5qa2 |
| not modelled | 5.2 | 23 | Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Homoserine dehydrogenase-like
43 | c1hvwA_ |
| not modelled | 5.2 | 100 | PDB header:toxin Chain: A: PDB Molecule:omega-atracotoxin-hv1a; PDBTitle: hairpinless mutant of omega-atracotoxin-hv1a
44 | d1hvwa_ |
| not modelled | 5.2 | 100 | Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins

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