Phyre 2 Results for O14468

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Email | l.a.kelley@imperial.ac.uk
Description | O14468
Date | Mon Jul 2 19:10:22 BST 2012
Unique Job ID | 0c65ad757a21c736

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1xppa_
Top template information
Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RBP11/RpoL
Confidence and coverage
Confidence: | 38.4% | Coverage: | 37%
28 residues ( 37% of your sequence) have been modelled with 38.4% 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 | S | T | E | K | L | E | A | S | E | E | P | Q | A | P | L | A | N | T | S | E | T | N | S | I | K | G | D | T | E | N | I | V | T | V | F | D | L | A | N | E | I | E | K | S | L | K | D | V | Q | R | Q | M | K | E | N | D | D | E | F
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Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |
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Sequence |  | S | R | S | I | Q | A | I | E | D | K | L | N | K | M | S | R
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 |
| d1xppa_ |

### PDB 1xpp chain A

Region: 42 - 69
Aligned: 28
Modelled: 28
Confidence: 38.4%
Identity: 14%
Fold: DCoH-like
Superfamily: RBP11-like subunits of RNA polymerase
Family: RBP11/RpoL

Phyre2
2 |
| c3pvpA_ |

### PDB 3pvp chain A

Region: 40 - 76
Aligned: 36
Modelled: 37
Confidence: 35.9%
Identity: 11%
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna

Phyre2
3 |
| c1m1jA_ |

### PDB 1m1j chain A

Region: 34 - 74
Aligned: 41
Modelled: 41
Confidence: 30.4%
Identity: 12%
PDB header:blood clotting
Chain: A: PDB Molecule:fibrinogen alpha subunit;
PDBTitle: crystal structure of native chicken fibrinogen with two different2 bound ligands

Phyre2
4 |
| d1slqa_ |

### PDB 1slq chain A

Region: 6 - 55
Aligned: 34
Modelled: 35
Confidence: 26.7%
Identity: 26%
Fold: VP4 membrane interaction domain
Superfamily: VP4 membrane interaction domain
Family: VP4 membrane interaction domain

Phyre2
5 |
| c3kypA_ |

### PDB 3kyp chain A

Region: 46 - 76
Aligned: 31
Modelled: 31
Confidence: 21.2%
Identity: 13%
PDB header:chaperone
Chain: A: PDB Molecule:nucleosome assembly protein;
PDBTitle: crystal structure of nucleosome assembly protein s (pfnaps) from2 plasmodium falciparum

Phyre2
6 |
| d1j1va_ |

### PDB 1j1v chain A

Region: 40 - 72
Aligned: 32
Modelled: 33
Confidence: 13.2%
Identity: 6%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: TrpR-like
Family: Chromosomal replication initiation factor DnaA C-terminal domain IV

Phyre2
7 |
| c3m06F_ |

### PDB 3m06 chain F

Region: 30 - 76
Aligned: 44
Modelled: 47
Confidence: 13.1%
Identity: 27%
PDB header:protein binding
Chain: F: PDB Molecule:tnf receptor-associated factor 2;
PDBTitle: crystal structure of traf2

Phyre2
8 |
| c3gyvA_ |

### PDB 3gyv chain A

Region: 44 - 74
Aligned: 31
Modelled: 31
Confidence: 11.6%
Identity: 19%
PDB header:chaperone
Chain: A: PDB Molecule:nucleosome assembly protein 1, putative;
PDBTitle: crystal structure of nucleosome assembly protein from plasmodium2 falciparum

Phyre2
9 |
| d2ayua1 |

### PDB 2ayu chain A domain 1

Region: 44 - 74
Aligned: 31
Modelled: 31
Confidence: 11.3%
Identity: 29%
Fold: NAP-like
Superfamily: NAP-like
Family: NAP-like

Phyre2
10 |
| c2ayuA_ |

### PDB 2ayu chain A

Region: 44 - 74
Aligned: 31
Modelled: 31
Confidence: 11.3%
Identity: 29%
PDB header:chaperone
Chain: A: PDB Molecule:nucleosome assembly protein;
PDBTitle: the structure of nucleosome assembly protein suggests a mechanism for2 histone binding and shuttling

Phyre2
11 |
| d1nu9c1 |

### PDB 1nu9 chain C domain 1

Region: 22 - 61
Aligned: 40
Modelled: 40
Confidence: 11.2%
Identity: 28%
Fold: immunoglobulin/albumin-binding domain-like
Superfamily: Staphylocoagulase
Family: Staphylocoagulase

Phyre2
12 |
| c3m0dC_ |

### PDB 3m0d chain C

Region: 30 - 76
Aligned: 44
Modelled: 47
Confidence: 10.7%
Identity: 27%
PDB header:signaling protein
Chain: C: PDB Molecule:tnf receptor-associated factor 1;
PDBTitle: crystal structure of the traf1:traf2:ciap2 complex

Phyre2
13 |
| d1nd9a_ |

### PDB 1nd9 chain A

Region: 33 - 55
Aligned: 23
Modelled: 23
Confidence: 10.4%
Identity: 30%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: N-terminal subdomain of bacterial translation initiation factor IF2

Phyre2
14 |
| c2xzrA_ |

### PDB 2xzr chain A

Region: 46 - 74
Aligned: 25
Modelled: 29
Confidence: 10.1%
Identity: 44%
PDB header:cell adhesion
Chain: A: PDB Molecule:immunoglobulin-binding protein eibd;
PDBTitle: escherichia coli immunoglobulin-binding protein eibd 391-438 fused2 to gcn4 adaptors

Phyre2
15 |
| c2hn1A_ |

### PDB 2hn1 chain A

Region: 34 - 76
Aligned: 43
Modelled: 43
Confidence: 9.3%
Identity: 9%
PDB header:metal transport
Chain: A: PDB Molecule:magnesium and cobalt transporter;
PDBTitle: crystal structure of a cora soluble domain from a. fulgidus in complex2 with co2+

Phyre2
16 |
| c2c5iT_ |

### PDB 2c5i chain T

Region: 26 - 74
Aligned: 49
Modelled: 49
Confidence: 8.5%
Identity: 20%
PDB header:protein transport
Chain: T: PDB Molecule:t-snare affecting a late golgi compartment
PDBTitle: n-terminal domain of tlg1 complexed with n-terminus of2 vps51 in distorted conformation

Phyre2
17 |
| c1pl5A_ |

### PDB 1pl5 chain A

Region: 43 - 64
Aligned: 22
Modelled: 22
Confidence: 8.4%
Identity: 23%
PDB header:dna binding protein/transcription
Chain: A: PDB Molecule:regulatory protein sir4;
PDBTitle: crystal structure analysis of the sir4p c-terminal coiled2 coil

Phyre2
18 |
| c1nyhA_ |

### PDB 1nyh chain A

Region: 43 - 64
Aligned: 22
Modelled: 22
Confidence: 8.3%
Identity: 23%
PDB header:transcription repressor
Chain: A: PDB Molecule:regulatory protein sir4;
PDBTitle: crystal structure of the coiled-coil dimerization motif of sir4

Phyre2
19 |
| d1wtya_ |

### PDB 1wty chain A

Region: 42 - 68
Aligned: 27
Modelled: 27
Confidence: 7.8%
Identity: 26%
Fold: Four-helical up-and-down bundle
Superfamily: Nucleotidyltransferase substrate binding subunit/domain
Family: Family 1 bi-partite nucleotidyltransferase subunit

Phyre2
20 |
| c1x8yA_ |

### PDB 1x8y chain A

Region: 42 - 74
Aligned: 33
Modelled: 33
Confidence: 7.7%
Identity: 21%
PDB header:structural protein
Chain: A: PDB Molecule:lamin a/c;
PDBTitle: human lamin coil 2b

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1xppa_ |
|  | 38.4 | 14 | Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RBP11/RpoL
2 | c3pvpA_ |
|  | 35.9 | 11 | PDB header:dna binding protein/dna Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna
3 | c1m1jA_ |
|  | 30.4 | 12 | PDB header:blood clotting Chain: A: PDB Molecule:fibrinogen alpha subunit; PDBTitle: crystal structure of native chicken fibrinogen with two different2 bound ligands
4 | d1slqa_ |
|  | 26.7 | 26 | Fold:VP4 membrane interaction domain Superfamily:VP4 membrane interaction domain Family:VP4 membrane interaction domain
5 | c3kypA_ |
|  | 21.2 | 13 | PDB header:chaperone Chain: A: PDB Molecule:nucleosome assembly protein; PDBTitle: crystal structure of nucleosome assembly protein s (pfnaps) from2 plasmodium falciparum
6 | d1j1va_ |
|  | 13.2 | 6 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Chromosomal replication initiation factor DnaA C-terminal domain IV
7 | c3m06F_ |
|  | 13.1 | 27 | PDB header:protein binding Chain: F: PDB Molecule:tnf receptor-associated factor 2; PDBTitle: crystal structure of traf2
8 | c3gyvA_ |
|  | 11.6 | 19 | PDB header:chaperone Chain: A: PDB Molecule:nucleosome assembly protein 1, putative; PDBTitle: crystal structure of nucleosome assembly protein from plasmodium2 falciparum
9 | d2ayua1 |
|  | 11.3 | 29 | Fold:NAP-like Superfamily:NAP-like Family:NAP-like
10 | c2ayuA_ |
|  | 11.3 | 29 | PDB header:chaperone Chain: A: PDB Molecule:nucleosome assembly protein; PDBTitle: the structure of nucleosome assembly protein suggests a mechanism for2 histone binding and shuttling
11 | d1nu9c1 |
|  | 11.2 | 28 | Fold:immunoglobulin/albumin-binding domain-like Superfamily:Staphylocoagulase Family:Staphylocoagulase
12 | c3m0dC_ |
|  | 10.7 | 27 | PDB header:signaling protein Chain: C: PDB Molecule:tnf receptor-associated factor 1; PDBTitle: crystal structure of the traf1:traf2:ciap2 complex
13 | d1nd9a_ |
|  | 10.4 | 30 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:N-terminal subdomain of bacterial translation initiation factor IF2
14 | c2xzrA_ |
|  | 10.1 | 44 | PDB header:cell adhesion Chain: A: PDB Molecule:immunoglobulin-binding protein eibd; PDBTitle: escherichia coli immunoglobulin-binding protein eibd 391-438 fused2 to gcn4 adaptors
15 | c2hn1A_ |
|  | 9.3 | 9 | PDB header:metal transport Chain: A: PDB Molecule:magnesium and cobalt transporter; PDBTitle: crystal structure of a cora soluble domain from a. fulgidus in complex2 with co2+
16 | c2c5iT_ |
|  | 8.5 | 20 | PDB header:protein transport Chain: T: PDB Molecule:t-snare affecting a late golgi compartment PDBTitle: n-terminal domain of tlg1 complexed with n-terminus of2 vps51 in distorted conformation
17 | c1pl5A_ |
|  | 8.4 | 23 | PDB header:dna binding protein/transcription Chain: A: PDB Molecule:regulatory protein sir4; PDBTitle: crystal structure analysis of the sir4p c-terminal coiled2 coil
18 | c1nyhA_ |
|  | 8.3 | 23 | PDB header:transcription repressor Chain: A: PDB Molecule:regulatory protein sir4; PDBTitle: crystal structure of the coiled-coil dimerization motif of sir4
19 | d1wtya_ |
|  | 7.8 | 26 | Fold:Four-helical up-and-down bundle Superfamily:Nucleotidyltransferase substrate binding subunit/domain Family:Family 1 bi-partite nucleotidyltransferase subunit
20 | c1x8yA_ |
|  | 7.7 | 21 | PDB header:structural protein Chain: A: PDB Molecule:lamin a/c; PDBTitle: human lamin coil 2b
21 | c3b5nE_ |
| not modelled | 7.7 | 13 | PDB header:membrane protein Chain: E: PDB Molecule:synaptobrevin homolog 1; PDBTitle: structure of the yeast plasma membrane snare complex
22 | c3hfdA_ |
| not modelled | 7.5 | 19 | PDB header:chaperone, protein transport Chain: A: PDB Molecule:nucleosome assembly protein 1; PDBTitle: nucleosome assembly protein 1 from plasmodium knowlesi
23 | d1t72a_ |
| not modelled | 6.8 | 10 | Fold:Spectrin repeat-like Superfamily:PhoU-like Family:PhoU-like
24 | c2ovcA_ |
| not modelled | 6.4 | 24 | PDB header:transport protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily kqt member 4; PDBTitle: crystal structure of a coiled-coil tetramerization domain from kv7.42 channels
25 | d1oyia_ |
| not modelled | 6.3 | 50 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain
26 | c1oyiA_ |
| not modelled | 6.3 | 50 | PDB header:viral protein Chain: A: PDB Molecule:double-stranded rna-binding protein; PDBTitle: solution structure of the z-dna binding domain of the2 vaccinia virus gene e3l
27 | c1uixA_ |
| not modelled | 6.1 | 19 | PDB header:transferase Chain: A: PDB Molecule:rho-associated kinase; PDBTitle: coiled-coil structure of the rhoa-binding domain in rho-2 kinase
28 | c3kyiA_ |
| not modelled | 5.8 | 21 | PDB header:transferase Chain: A: PDB Molecule:putative histidine protein kinase; PDBTitle: crystal structure of the phosphorylated p1 domain of chea3 in complex2 with chey6 from r. sphaeroides
29 | c1unyA_ |
| not modelled | 5.7 | 45 | PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles

Binding site prediction |

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