Phyre 2 Results for P64467

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Email | l.a.kelley@imperial.ac.uk
Description | P64467
Date | Thu Jan 5 12:08:38 GMT 2012
Unique Job ID | 462c7feb13bc9836

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template d1jw2a_
Top template information
Fold:Open three-helical up-and-down bundle Superfamily:Hemolysin expression modulating protein HHA Family:Hemolysin expression modulating protein HHA
Confidence and coverage
Confidence: | 100.0% | Coverage: | 94%
67 residues ( 94% 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 | V | Q | D | Y | L | L | K | F | R | K | I | S | S | L | E | S | L | E | K | L | Y | D | H | L | N | Y | T | L | T | D | D | Q | E | L | I | N | M | Y | R | A | A | D | H | R | R | A | E | L | V | S | G | G | R | L | F | D | L | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | .
Sequence |  | Q | V | P | K | S | V | W | H | Y | V | Q
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 |
| d1jw2a_ |

### PDB 1jw2 chain A

Region: 1 - 71
Aligned: 67
Modelled: 71
Confidence: 100.0%
Identity: 40%
Fold: Open three-helical up-and-down bundle
Superfamily: Hemolysin expression modulating protein HHA
Family: Hemolysin expression modulating protein HHA

Phyre2
2 |
| c2jqtA_ |

### PDB 2jqt chain A

Region: 1 - 57
Aligned: 57
Modelled: 57
Confidence: 99.9%
Identity: 100%
PDB header:protein binding
Chain: A: PDB Molecule:h-ns/stpa-binding protein 2;
PDBTitle: structure of the bacterial replication origin-associated2 protein cnu

Phyre2
3 |
| c2jpnA_ |

### PDB 2jpn chain A

Region: 5 - 50
Aligned: 45
Modelled: 46
Confidence: 36.6%
Identity: 31%
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase uvsw;
PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1

Phyre2
4 |
| c3jvoA_ |

### PDB 3jvo chain A

Region: 18 - 70
Aligned: 53
Modelled: 53
Confidence: 31.9%
Identity: 21%
PDB header:viral protein
Chain: A: PDB Molecule:gp6;
PDBTitle: crystal structure of bacteriophage hk97 gp6

Phyre2
5 |
| d1lr1a_ |

### PDB 1lr1 chain A

Region: 7 - 42
Aligned: 36
Modelled: 36
Confidence: 28.0%
Identity: 25%
Fold: H-NS histone-like proteins
Superfamily: H-NS histone-like proteins
Family: H-NS histone-like proteins

Phyre2
6 |
| c3ke4B_ |

### PDB 3ke4 chain B

Region: 16 - 70
Aligned: 54
Modelled: 55
Confidence: 25.2%
Identity: 31%
PDB header:transferase
Chain: B: PDB Molecule:hypothetical cytosolic protein;
PDBTitle: crystal structure of a pduo-type atp:cob(i)alamin adenosyltransferase2 from bacillus cereus

Phyre2
7 |
| c2idxA_ |

### PDB 2idx chain A

Region: 16 - 70
Aligned: 54
Modelled: 55
Confidence: 23.6%
Identity: 26%
PDB header:transferase
Chain: A: PDB Molecule:cob(i)yrinic acid a,c-diamide
PDBTitle: structure of human atp:cobalamin adenosyltransferase bound2 to atp.

Phyre2
8 |
| d1trra_ |

### PDB 1trr chain A

Region: 4 - 62
Aligned: 54
Modelled: 59
Confidence: 23.5%
Identity: 20%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: TrpR-like
Family: Trp repressor, TrpR

Phyre2
9 |
| d1ej2a_ |

### PDB 1ej2 chain A

Region: 47 - 71
Aligned: 23
Modelled: 25
Confidence: 21.8%
Identity: 22%
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Nucleotidylyl transferase
Family: Adenylyltransferase

Phyre2
10 |
| d1jhga_ |

### PDB 1jhg chain A

Region: 4 - 62
Aligned: 54
Modelled: 59
Confidence: 12.8%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: TrpR-like
Family: Trp repressor, TrpR

Phyre2
11 |
| c3cvfA_ |

### PDB 3cvf chain A

Region: 18 - 59
Aligned: 41
Modelled: 42
Confidence: 11.8%
Identity: 27%
PDB header:signaling protein
Chain: A: PDB Molecule:homer protein homolog 3;
PDBTitle: crystal structure of the carboxy terminus of homer3

Phyre2
12 |
| c3d0jA_ |

### PDB 3d0j chain A

Region: 54 - 70
Aligned: 14
Modelled: 17
Confidence: 10.6%
Identity: 36%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein ca_c3497;
PDBTitle: crystal structure of conserved protein of unknown function ca_c34972 from clostridium acetobutylicum atcc 824

Phyre2
13 |
| c2g2dA_ |

### PDB 2g2d chain A

Region: 16 - 70
Aligned: 53
Modelled: 55
Confidence: 10.3%
Identity: 28%
PDB header:transferase
Chain: A: PDB Molecule:atp:cobalamin adenosyltransferase;
PDBTitle: crystal structure of a putative pduo-type atp:cobalamin2 adenosyltransferase from mycobacterium tuberculosis

Phyre2
14 |
| c3cm8A_ |

### PDB 3cm8 chain A

Region: 3 - 24
Aligned: 22
Modelled: 22
Confidence: 9.8%
Identity: 18%
PDB header:rna binding protein/transferase
Chain: A: PDB Molecule:polymerase acidic protein;
PDBTitle: a rna polymerase subunit structure from virus

Phyre2
15 |
| d1t07a_ |

### PDB 1t07 chain A

Region: 49 - 68
Aligned: 16
Modelled: 20
Confidence: 9.7%
Identity: 19%
Fold: YggX-like
Superfamily: YggX-like
Family: YggX-like

Phyre2
16 |
| d1xs8a_ |

### PDB 1xs8 chain A

Region: 49 - 68
Aligned: 16
Modelled: 20
Confidence: 9.4%
Identity: 38%
Fold: YggX-like
Superfamily: YggX-like
Family: YggX-like

Phyre2
17 |
| c3i5qA_ |

### PDB 3i5q chain A

Region: 15 - 51
Aligned: 37
Modelled: 37
Confidence: 9.3%
Identity: 24%
PDB header:protein transport
Chain: A: PDB Molecule:nucleoporin nup170;
PDBTitle: nup170(aa1253-1502) at 2.2 a, s.cerevisiae

Phyre2
18 |
| c2rbgB_ |

### PDB 2rbg chain B

Region: 51 - 66
Aligned: 14
Modelled: 16
Confidence: 8.9%
Identity: 21%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative uncharacterized protein st0493;
PDBTitle: crystal structure of hypothetical protein(st0493) from2 sulfolobus tokodaii

Phyre2
19 |
| c1nybA_ |

### PDB 1nyb chain A

Region: 41 - 52
Aligned: 12
Modelled: 12
Confidence: 8.5%
Identity: 42%
PDB header:transcription/rna
Chain: A: PDB Molecule:probable regulatory protein n;
PDBTitle: solution structure of the bacteriophage phi21 n peptide-boxb2 rna complex

Phyre2
20 |
| d1dd4c_ |

### PDB 1dd4 chain C

Region: 18 - 61
Aligned: 27
Modelled: 44
Confidence: 8.4%
Identity: 26%
Fold: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily: Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family: Ribosomal protein L7/12, oligomerisation (N-terminal) domain

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1jw2a_ |
|  | 100.0 | 40 | Fold:Open three-helical up-and-down bundle Superfamily:Hemolysin expression modulating protein HHA Family:Hemolysin expression modulating protein HHA
2 | c2jqtA_ |
|  | 99.9 | 100 | PDB header:protein binding Chain: A: PDB Molecule:h-ns/stpa-binding protein 2; PDBTitle: structure of the bacterial replication origin-associated2 protein cnu
3 | c2jpnA_ |
|  | 36.6 | 31 | PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent dna helicase uvsw; PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1
4 | c3jvoA_ |
|  | 31.9 | 21 | PDB header:viral protein Chain: A: PDB Molecule:gp6; PDBTitle: crystal structure of bacteriophage hk97 gp6
5 | d1lr1a_ |
|  | 28.0 | 25 | Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins
6 | c3ke4B_ |
|  | 25.2 | 31 | PDB header:transferase Chain: B: PDB Molecule:hypothetical cytosolic protein; PDBTitle: crystal structure of a pduo-type atp:cob(i)alamin adenosyltransferase2 from bacillus cereus
7 | c2idxA_ |
|  | 23.6 | 26 | PDB header:transferase Chain: A: PDB Molecule:cob(i)yrinic acid a,c-diamide PDBTitle: structure of human atp:cobalamin adenosyltransferase bound2 to atp.
8 | d1trra_ |
|  | 23.5 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
9 | d1ej2a_ |
|  | 21.8 | 22 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
10 | d1jhga_ |
|  | 12.8 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR
11 | c3cvfA_ |
|  | 11.8 | 27 | PDB header:signaling protein Chain: A: PDB Molecule:homer protein homolog 3; PDBTitle: crystal structure of the carboxy terminus of homer3
12 | c3d0jA_ |
|  | 10.6 | 36 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ca_c3497; PDBTitle: crystal structure of conserved protein of unknown function ca_c34972 from clostridium acetobutylicum atcc 824
13 | c2g2dA_ |
|  | 10.3 | 28 | PDB header:transferase Chain: A: PDB Molecule:atp:cobalamin adenosyltransferase; PDBTitle: crystal structure of a putative pduo-type atp:cobalamin2 adenosyltransferase from mycobacterium tuberculosis
14 | c3cm8A_ |
|  | 9.8 | 18 | PDB header:rna binding protein/transferase Chain: A: PDB Molecule:polymerase acidic protein; PDBTitle: a rna polymerase subunit structure from virus
15 | d1t07a_ |
|  | 9.7 | 19 | Fold:YggX-like Superfamily:YggX-like Family:YggX-like
16 | d1xs8a_ |
|  | 9.4 | 38 | Fold:YggX-like Superfamily:YggX-like Family:YggX-like
17 | c3i5qA_ |
|  | 9.3 | 24 | PDB header:protein transport Chain: A: PDB Molecule:nucleoporin nup170; PDBTitle: nup170(aa1253-1502) at 2.2 a, s.cerevisiae
18 | c2rbgB_ |
|  | 8.9 | 21 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative uncharacterized protein st0493; PDBTitle: crystal structure of hypothetical protein(st0493) from2 sulfolobus tokodaii
19 | c1nybA_ |
|  | 8.5 | 42 | PDB header:transcription/rna Chain: A: PDB Molecule:probable regulatory protein n; PDBTitle: solution structure of the bacteriophage phi21 n peptide-boxb2 rna complex
20 | d1dd4c_ |
|  | 8.4 | 26 | Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain
21 | d1od6a_ |
| not modelled | 8.2 | 14 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
22 | c2nt8A_ |
| not modelled | 7.8 | 24 | PDB header:transferase Chain: A: PDB Molecule:cobalamin adenosyltransferase; PDBTitle: atp bound at the active site of a pduo type atp:co(i)rrinoid2 adenosyltransferase from lactobacillus reuteri
23 | c2zhzC_ |
| not modelled | 7.7 | 31 | PDB header:transferase Chain: C: PDB Molecule:atp:cob(i)alamin adenosyltransferase, putative; PDBTitle: crystal structure of a pduo-type atp:cobalamin adenosyltransferase2 from burkholderia thailandensis
24 | c3nd5D_ |
| not modelled | 7.5 | 18 | PDB header:transferase Chain: D: PDB Molecule:phosphopantetheine adenylyltransferase; PDBTitle: crystal structure of phosphopantetheine adenylyltransferase (ppat)2 from enterococcus faecalis
25 | d1vlha_ |
| not modelled | 7.5 | 21 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
26 | d1ni8a_ |
| not modelled | 7.2 | 21 | Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins
27 | d1uhra_ |
| not modelled | 7.1 | 21 | Fold:SWIB/MDM2 domain Superfamily:SWIB/MDM2 domain Family:SWIB/MDM2 domain
28 | c2h29A_ |
| not modelled | 7.0 | 60 | PDB header:transferase Chain: A: PDB Molecule:probable nicotinate-nucleotide PDBTitle: crystal structure of nicotinic acid mononucleotide2 adenylyltransferase from staphylococcus aureus: product3 bound form 1
29 | c3frwF_ |
| not modelled | 7.0 | 19 | PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
30 | d1f3ua_ |
| not modelled | 6.7 | 40 | Fold:triple barrel Superfamily:Rap30/74 interaction domains Family:Rap30/74 interaction domains
31 | d1tfua_ |
| not modelled | 6.4 | 14 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
32 | d1i27a_ |
| not modelled | 6.1 | 38 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of the rap74 subunit of TFIIF
33 | d1v31a_ |
| not modelled | 5.9 | 21 | Fold:SWIB/MDM2 domain Superfamily:SWIB/MDM2 domain Family:SWIB/MDM2 domain
34 | c1dd3D_ |
| not modelled | 5.9 | 26 | PDB header:ribosome Chain: D: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: crystal structure of ribosomal protein l12 from thermotoga maritima
35 | c1dd3C_ |
| not modelled | 5.9 | 26 | PDB header:ribosome Chain: C: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: crystal structure of ribosomal protein l12 from thermotoga maritima
36 | c3f3mA_ |
| not modelled | 5.7 | 11 | PDB header:transferase Chain: A: PDB Molecule:phosphopantetheine adenylyltransferase; PDBTitle: six crystal structures of two phosphopantetheine2 adenylyltransferases reveal an alternative ligand binding3 mode and an associated structural change
37 | d1o6ba_ |
| not modelled | 5.7 | 18 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
38 | c2l3lA_ |
| not modelled | 5.6 | 20 | PDB header:chaperone Chain: A: PDB Molecule:tubulin-specific chaperone c; PDBTitle: the solution structure of the n-terminal domain of human tubulin2 binding cofactor c reveals a platform for the interaction with ab-3 tubulin
39 | c1zawV_ |
| not modelled | 5.5 | 26 | PDB header:structural protein Chain: V: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a
40 | c2kngA_ |
| not modelled | 5.5 | 33 | PDB header:dna binding protein Chain: A: PDB Molecule:protein lsr2; PDBTitle: solution structure of c-domain of lsr2
41 | c3korD_ |
| not modelled | 5.4 | 18 | PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
42 | d1qjca_ |
| not modelled | 5.3 | 11 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Adenylyltransferase
43 | c1zawW_ |
| not modelled | 5.3 | 26 | PDB header:structural protein Chain: W: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a
44 | c1zawU_ |
| not modelled | 5.3 | 26 | PDB header:structural protein Chain: U: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a
45 | c1xhmB_ |
| not modelled | 5.2 | 27 | PDB header:signaling protein Chain: B: PDB Molecule:guanine nucleotide-binding protein g(i)/g(s) PDBTitle: the crystal structure of a biologically active peptide2 (sigk) bound to a g protein beta:gamma heterodimer
46 | c1zaxV_ |
| not modelled | 5.1 | 26 | PDB header:structural protein Chain: V: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form b
47 | c1zavV_ |
| not modelled | 5.1 | 26 | PDB header:structural protein Chain: V: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p21
48 | c1zaxY_ |
| not modelled | 5.1 | 26 | PDB header:structural protein Chain: Y: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form b
49 | c1zavW_ |
| not modelled | 5.1 | 26 | PDB header:structural protein Chain: W: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p21
50 | c1zaxW_ |
| not modelled | 5.1 | 26 | PDB header:structural protein Chain: W: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form b
51 | c1zavX_ |
| not modelled | 5.1 | 26 | PDB header:structural protein Chain: X: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p21

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
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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