Phyre 2 Results for C0Z3X9

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | C0Z3X9
Date | Thu Jan 5 10:55:44 GMT 2012
Unique Job ID | bd3fcbc4bee13106

Summary |

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

Model (left) based on template d2qxfa1
Top template information
Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
Confidence and coverage
Confidence: | 100.0% | Coverage: | 92%
82 residues ( 92% 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 |

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Sequence |  | M | T | D | T | D | K | Q | P | T | F | L | F | H | D | Y | E | T | F | G | T | H | P | A | L | D | R | P | A | Q | F | A | A | I | R | T | D | S | E | F | N | V | I | G | E | P | E | V | F | Y | C | K | P | A | D | D | Y | L | P | Q | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | .
Sequence |  | G | A | V | L | I | T | G | I | T | P | Q | E | A | R | A | K | G | E | N | E | A | A | F | A | A | R | I | H | S
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 |
| d2qxfa1 |

### PDB 2qxf chain A domain 1

Region: 7 - 88
Aligned: 82
Modelled: 82
Confidence: 100.0%
Identity: 99%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
2 |
| d1y97a1 |

### PDB 1y97 chain A domain 1

Region: 3 - 87
Aligned: 85
Modelled: 85
Confidence: 99.8%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
3 |
| d2f96a1 |

### PDB 2f96 chain A domain 1

Region: 5 - 87
Aligned: 83
Modelled: 83
Confidence: 99.8%
Identity: 24%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
4 |
| c3u6fA_ |

### PDB 3u6f chain A

Region: 3 - 87
Aligned: 85
Modelled: 84
Confidence: 99.8%
Identity: 22%
PDB header:hydrolase/dna
Chain: A: PDB Molecule:three prime repair exonuclease 1;
PDBTitle: mouse trex1 d200n mutant

Phyre2
5 |
| c3tr8A_ |

### PDB 3tr8 chain A

Region: 5 - 87
Aligned: 82
Modelled: 83
Confidence: 99.8%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:oligoribonuclease;
PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii

Phyre2
6 |
| d1j9aa_ |

### PDB 1j9a chain A

Region: 3 - 88
Aligned: 85
Modelled: 85
Confidence: 99.8%
Identity: 19%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
7 |
| d3b6oa1 |

### PDB 3b6o chain A domain 1

Region: 6 - 87
Aligned: 82
Modelled: 82
Confidence: 99.8%
Identity: 22%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
8 |
| c3cm6A_ |

### PDB 3cm6 chain A

Region: 9 - 87
Aligned: 78
Modelled: 79
Confidence: 99.8%
Identity: 24%
PDB header:hydrolase, apoptosis
Chain: A: PDB Molecule:cell death-related nuclease 4;
PDBTitle: crystal structure of cell-death related nuclease 4 (crn-4)2 bound with er

Phyre2
9 |
| d1w0ha_ |

### PDB 1w0h chain A

Region: 9 - 88
Aligned: 79
Modelled: 80
Confidence: 99.8%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
10 |
| c2xriA_ |

### PDB 2xri chain A

Region: 3 - 88
Aligned: 85
Modelled: 86
Confidence: 99.8%
Identity: 15%
PDB header:hydrolase
Chain: A: PDB Molecule:eri1 exoribonuclease 3;
PDBTitle: crystal structure of human eri1 exoribonuclease 3

Phyre2
11 |
| c2gbzA_ |

### PDB 2gbz chain A

Region: 7 - 88
Aligned: 81
Modelled: 82
Confidence: 99.8%
Identity: 17%
PDB header:hydrolase
Chain: A: PDB Molecule:oligoribonuclease;
PDBTitle: the crystal structure of xc847 from xanthomonas campestris: a 3-52 oligoribonuclease of dnaq fold family with a novel opposingly-shifted3 helix

Phyre2
12 |
| d2igia1 |

### PDB 2igi chain A domain 1

Region: 4 - 89
Aligned: 85
Modelled: 86
Confidence: 99.8%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
13 |
| c1zbhA_ |

### PDB 1zbh chain A

Region: 9 - 88
Aligned: 79
Modelled: 80
Confidence: 99.7%
Identity: 13%
PDB header:hydrolase/rna
Chain: A: PDB Molecule:3'-5' exonuclease eri1;
PDBTitle: 3'-end specific recognition of histone mrna stem-loop by 3'-2 exonuclease

Phyre2
14 |
| c1zbuB_ |

### PDB 1zbu chain B

Region: 9 - 87
Aligned: 78
Modelled: 79
Confidence: 99.7%
Identity: 13%
PDB header:hydrolase
Chain: B: PDB Molecule:3'-5' exonuclease eri1;
PDBTitle: crystal structure of full-length 3'-exonuclease

Phyre2
15 |
| d2guia1 |

### PDB 2gui chain A domain 1

Region: 9 - 87
Aligned: 75
Modelled: 79
Confidence: 99.7%
Identity: 20%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
16 |
| c2p1jB_ |

### PDB 2p1j chain B

Region: 9 - 87
Aligned: 74
Modelled: 79
Confidence: 99.7%
Identity: 23%
PDB header:transferase
Chain: B: PDB Molecule:dna polymerase iii polc-type;
PDBTitle: crystal structure of a polc-type dna polymerase iii2 exonuclease domain from thermotoga maritima

Phyre2
17 |
| d1wlja_ |

### PDB 1wlj chain A

Region: 9 - 88
Aligned: 72
Modelled: 80
Confidence: 99.5%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
18 |
| c2is3B_ |

### PDB 2is3 chain B

Region: 5 - 75
Aligned: 52
Modelled: 71
Confidence: 98.3%
Identity: 13%
PDB header:hydrolase
Chain: B: PDB Molecule:ribonuclease t;
PDBTitle: crystal structure of escherichia coli rnase t

Phyre2
19 |
| d1uoca_ |

### PDB 1uoc chain A

Region: 6 - 89
Aligned: 83
Modelled: 84
Confidence: 98.1%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: CAF1-like ribonuclease

Phyre2
20 |
| d1x9ma1 |

### PDB 1x9m chain A domain 1

Region: 10 - 38
Aligned: 29
Modelled: 29
Confidence: 97.4%
Identity: 7%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: DnaQ-like 3'-5' exonuclease

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d2qxfa1 |
|  | 100.0 | 99 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
2 | d1y97a1 |
|  | 99.8 | 16 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
3 | d2f96a1 |
|  | 99.8 | 24 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
4 | c3u6fA_ |
|  | 99.8 | 22 | PDB header:hydrolase/dna Chain: A: PDB Molecule:three prime repair exonuclease 1; PDBTitle: mouse trex1 d200n mutant
5 | c3tr8A_ |
|  | 99.8 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii
6 | d1j9aa_ |
|  | 99.8 | 19 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
7 | d3b6oa1 |
|  | 99.8 | 22 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
8 | c3cm6A_ |
|  | 99.8 | 24 | PDB header:hydrolase, apoptosis Chain: A: PDB Molecule:cell death-related nuclease 4; PDBTitle: crystal structure of cell-death related nuclease 4 (crn-4)2 bound with er
9 | d1w0ha_ |
|  | 99.8 | 15 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
10 | c2xriA_ |
|  | 99.8 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:eri1 exoribonuclease 3; PDBTitle: crystal structure of human eri1 exoribonuclease 3
11 | c2gbzA_ |
|  | 99.8 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: the crystal structure of xc847 from xanthomonas campestris: a 3-52 oligoribonuclease of dnaq fold family with a novel opposingly-shifted3 helix
12 | d2igia1 |
|  | 99.8 | 15 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
13 | c1zbhA_ |
|  | 99.7 | 13 | PDB header:hydrolase/rna Chain: A: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: 3'-end specific recognition of histone mrna stem-loop by 3'-2 exonuclease
14 | c1zbuB_ |
|  | 99.7 | 13 | PDB header:hydrolase Chain: B: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: crystal structure of full-length 3'-exonuclease
15 | d2guia1 |
|  | 99.7 | 20 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
16 | c2p1jB_ |
|  | 99.7 | 23 | PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii polc-type; PDBTitle: crystal structure of a polc-type dna polymerase iii2 exonuclease domain from thermotoga maritima
17 | d1wlja_ |
|  | 99.5 | 17 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
18 | c2is3B_ |
|  | 98.3 | 13 | PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease t; PDBTitle: crystal structure of escherichia coli rnase t
19 | d1uoca_ |
|  | 98.1 | 18 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease
20 | d1x9ma1 |
|  | 97.4 | 7 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
21 | c2p51A_ |
| not modelled | 96.7 | 23 | PDB header:hydrolase, gene regulation Chain: A: PDB Molecule:spcc18.06c protein; PDBTitle: crystal structure of the s. pombe pop2p deadenylation2 subunit
22 | d1kfsa1 |
| not modelled | 96.4 | 9 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
23 | d2d5ra1 |
| not modelled | 96.1 | 16 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease
24 | d2hhva1 |
| not modelled | 96.1 | 9 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
25 | c2kzzA_ |
| not modelled | 95.7 | 19 | PDB header:transferase/dna Chain: A: PDB Molecule:protein (dna polymerase i); PDBTitle: klenow fragment with normal substrate and zinc only
26 | c1njzA_ |
| not modelled | 93.8 | 8 | PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase i; PDBTitle: cytosine-thymine mismatch at the polymerase active site
27 | c2a1sC_ |
| not modelled | 93.5 | 25 | PDB header:hydrolase Chain: C: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of native parn nuclease domain
28 | c1tk0A_ |
| not modelled | 92.8 | 7 | PDB header:transferase/electron transport/dna Chain: A: PDB Molecule:dna polymerase; PDBTitle: t7 dna polymerase ternary complex with 8 oxo guanosine and2 ddctp at the insertion site
29 | c3d45B_ |
| not modelled | 89.5 | 19 | PDB header:hydrolase Chain: B: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of mouse parn in complex with m7gpppg
30 | d1wn7a1 |
| not modelled | 89.2 | 22 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
31 | d1d5aa1 |
| not modelled | 83.9 | 15 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
32 | d1tgoa1 |
| not modelled | 81.0 | 24 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
33 | d1qhta1 |
| not modelled | 80.0 | 16 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
34 | c2gv9B_ |
| not modelled | 74.5 | 12 | PDB header:transferase Chain: B: PDB Molecule:dna polymerase; PDBTitle: crystal structure of the herpes simplex virus type 1 dna polymerase
35 | d1yt3a3 |
| not modelled | 65.2 | 11 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
36 | c3iayA_ |
| not modelled | 64.9 | 18 | PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase delta catalytic subunit; PDBTitle: ternary complex of dna polymerase delta
37 | c2vwkA_ |
| not modelled | 61.4 | 22 | PDB header:dna replication Chain: A: PDB Molecule:dna polymerase; PDBTitle: uracil recognition in archaeal dna polymerases captured by2 x-ray crystallography. v93q polymerase variant
38 | c4ktqA_ |
| not modelled | 58.8 | 17 | PDB header:transferase/dna Chain: A: PDB Molecule:protein (large fragment of dna polymerase i); PDBTitle: binary complex of the large fragment of dna polymerase i2 from t. aquaticus bound to a primer/template dna
39 | c2e6mA_ |
| not modelled | 53.9 | 12 | PDB header:hydrolase Chain: A: PDB Molecule:werner syndrome atp-dependent helicase homolog; PDBTitle: structure of mouse werner exonuclease domain
40 | c1yt3A_ |
| not modelled | 51.0 | 15 | PDB header:hydrolase,translation Chain: A: PDB Molecule:ribonuclease d; PDBTitle: crystal structure of escherichia coli rnase d, an2 exoribonuclease involved in structured rna processing
41 | c1d5aA_ |
| not modelled | 45.4 | 20 | PDB header:transferase Chain: A: PDB Molecule:protein (dna polymerase); PDBTitle: crystal structure of an archaebacterial dna polymerase2 d.tok. deposition of second native structure at 2.43 angstrom
42 | d1ih7a1 |
| not modelled | 27.7 | 20 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
43 | c2w0iA_ |
| not modelled | 17.6 | 10 | PDB header:transferase Chain: A: PDB Molecule:twinfilin-2; PDBTitle: structure of c-terminal actin depolymerizing factor2 homology (adf-h) domain of human twinfilin-2
44 | c2kd5A_ |
| not modelled | 13.2 | 13 | PDB header:hormone Chain: A: PDB Molecule:actin severing and dynamics regulatory protein; PDBTitle: solution structure of adf/cofilin (ldcof) from leishmania donovani
45 | d1ak7a_ |
| not modelled | 11.0 | 10 | Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like
46 | c3hhjA_ |
| not modelled | 10.7 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:mutator mutt protein; PDBTitle: crystal structure of mutator mutt from bartonella henselae
47 | c3cymA_ |
| not modelled | 10.6 | 22 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bad_0989; PDBTitle: crystal structure of protein bad_0989 from bifidobacterium2 adolescentis
48 | c2d3wB_ |
| not modelled | 10.2 | 18 | PDB header:biosynthetic protein Chain: B: PDB Molecule:probable atp-dependent transporter sufc; PDBTitle: crystal structure of escherichia coli sufc, an atpase2 compenent of the suf iron-sulfur cluster assembly machinery
49 | d2dk8a1 |
| not modelled | 9.6 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:RPO3F domain-like
50 | c2xfaA_ |
| not modelled | 9.3 | 10 | PDB header:protein binding Chain: A: PDB Molecule:actin depolymerization factor 2; PDBTitle: crystal structure of plasmodium berghei actin2 depolymerization factor 2
51 | d2hbka2 |
| not modelled | 8.5 | 15 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
52 | c2i2qA_ |
| not modelled | 8.4 | 10 | PDB header:actin-binding protein Chain: A: PDB Molecule:cofilin; PDBTitle: fission yeast cofilin
53 | d1q8ga_ |
| not modelled | 8.1 | 10 | Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like
54 | d1q8ia1 |
| not modelled | 6.5 | 14 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
55 | c3iydB_ |
| not modelled | 6.5 | 24 | PDB header:transcription/dna Chain: B: PDB Molecule:dna-directed rna polymerase subunit alpha; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex
56 | d1cnua_ |
| not modelled | 5.3 | 10 | Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Cofilin-like
57 | d1s5ja1 |
| not modelled | 5.3 | 12 | Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease
58 | c1s5jA_ |
| not modelled | 5.2 | 20 | PDB header:transferase Chain: A: PDB Molecule:dna polymerase i; PDBTitle: insight in dna replication: the crystal structure of dna2 polymerase b1 from the archaeon sulfolobus solfataricus

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