Phyre 2 Results for P76170

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Email | l.a.kelley@imperial.ac.uk
Description | P76170
Date | Thu Jan 5 12:20:04 GMT 2012
Unique Job ID | 0416c7293fe042f2

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2kmfA_
Top template information
PDB header:photosynthesis Chain: A: PDB Molecule:photosystem ii 11 kda protein; PDBTitle: solution structure of psb27 from cyanobacterial photosystem2 ii
Confidence and coverage
Confidence: | 30.8% | Coverage: | 21%
24 residues ( 21% of your sequence) have been modelled with 30.8% confidence by the single highest scoring template.
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | K | I | T | L | S | K | R | I | G | L | L | A | I | L | L | P | C | A | L | A | L | S | T | T | V | H | A | E | T | N | K | L | V | I | E | S | G | D | S | A | Q | S | R | Q | H | A | A | M | E | K | E | Q | W | N | D | T | R | N | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | .
Sequence |  | R | Q | K | V | N | K | R | T | E | K | E | W | D | K | A | D | A | A | F | D | N | R | D | K | C | E | Q | S | A | N | I | N | A | Y | W | E | P | N | T | L | R | C | L | D | R | R | T | G | R | V | I | T | P
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 |
| c2kmfA_ |

### PDB 2kmf chain A

Region: 57 - 80
Aligned: 24
Modelled: 24
Confidence: 30.8%
Identity: 25%
PDB header:photosynthesis
Chain: A: PDB Molecule:photosystem ii 11 kda protein;
PDBTitle: solution structure of psb27 from cyanobacterial photosystem2 ii

Phyre2
2 |
| c2vdaB_ |

### PDB 2vda chain B

Region: 1 - 28
Aligned: 28
Modelled: 28
Confidence: 27.7%
Identity: 36%
PDB header:protein transport
Chain: B: PDB Molecule:maltoporin;
PDBTitle: solution structure of the seca-signal peptide complex

Phyre2
3 |
| d1w6ua_ |

### PDB 1w6u chain A

Region: 7 - 60
Aligned: 54
Modelled: 54
Confidence: 21.8%
Identity: 22%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Tyrosine-dependent oxidoreductases

Phyre2
4 |
| c1p5lA_ |

### PDB 1p5l chain A

Region: 63 - 75
Aligned: 13
Modelled: 13
Confidence: 21.4%
Identity: 54%
PDB header:ribosome
Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1;
PDBTitle: hp (2-20) substitution phe5 to ser modification in sds-d252 micelles

Phyre2
5 |
| c1p5kA_ |

### PDB 1p5k chain A

Region: 63 - 75
Aligned: 13
Modelled: 13
Confidence: 20.0%
Identity: 54%
PDB header:ribosome
Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1;
PDBTitle: hp (2-20) substitution ser to leu11 modification in sds-d252 micelles

Phyre2
6 |
| d1txka2 |

### PDB 1txk chain A domain 2

Region: 86 - 99
Aligned: 14
Modelled: 14
Confidence: 14.3%
Identity: 50%
Fold: Supersandwich
Superfamily: Galactose mutarotase-like
Family: MdoG-like

Phyre2
7 |
| c1txkA_ |

### PDB 1txk chain A

Region: 86 - 99
Aligned: 14
Modelled: 14
Confidence: 13.2%
Identity: 50%
PDB header:biosynthetic protein
Chain: A: PDB Molecule:glucans biosynthesis protein g;
PDBTitle: crystal structure of escherichia coli opgg

Phyre2
8 |
| c1p0oA_ |

### PDB 1p0o chain A

Region: 63 - 75
Aligned: 13
Modelled: 13
Confidence: 13.0%
Identity: 54%
PDB header:ribosome
Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1;
PDBTitle: hp (2-20) substitution of trp for gln and asp at position2 17 and 19 modification in sds-d25 micelles

Phyre2
9 |
| c1p0jA_ |

### PDB 1p0j chain A

Region: 63 - 75
Aligned: 13
Modelled: 13
Confidence: 12.9%
Identity: 54%
PDB header:ribosome
Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1;
PDBTitle: hp (2-20) substitution asp to trp modification in sds-d252 micelles

Phyre2
10 |
| c1ot0A_ |

### PDB 1ot0 chain A

Region: 63 - 75
Aligned: 13
Modelled: 13
Confidence: 12.9%
Identity: 54%
PDB header:antibiotic
Chain: A: PDB Molecule:50s ribosomal protein l1;
PDBTitle: structure of antimicrobial peptide, hp (2-20) and its2 analogues derived from helicobacter pylori, as determined3 by 1h nmr spectroscopy

Phyre2
11 |
| c1p0lA_ |

### PDB 1p0l chain A

Region: 63 - 75
Aligned: 13
Modelled: 13
Confidence: 12.7%
Identity: 54%
PDB header:ribosome
Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1;
PDBTitle: hp (2-20) substitution gln to trp modification in sds-d252 micelles

Phyre2
12 |
| c1p0gA_ |

### PDB 1p0g chain A

Region: 63 - 75
Aligned: 13
Modelled: 13
Confidence: 12.6%
Identity: 54%
PDB header:ribosome
Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1;
PDBTitle: structure of antimicrobial peptide, hp (2-20) and its2 analogues derived from helicobacter pylori, as determined3 by 1h nmr spectroscopy

Phyre2
13 |
| c3gwnA_ |

### PDB 3gwn chain A

Region: 59 - 82
Aligned: 24
Modelled: 24
Confidence: 12.6%
Identity: 17%
PDB header:oxidoreductase
Chain: A: PDB Molecule:probable fad-linked sulfhydryl oxidase r596;
PDBTitle: crystal structure of the fad binding domain from mimivirus sulfhydryl2 oxidase r596

Phyre2
14 |
| c2yytA_ |

### PDB 2yyt chain A

Region: 28 - 55
Aligned: 28
Modelled: 28
Confidence: 12.0%
Identity: 21%
PDB header:lyase
Chain: A: PDB Molecule:orotidine 5'-phosphate decarboxylase;
PDBTitle: crystal structure of uncharacterized conserved protein from2 geobacillus kaustophilus

Phyre2
15 |
| d1t95a1 |

### PDB 1t95 chain A domain 1

Region: 99 - 113
Aligned: 15
Modelled: 15
Confidence: 10.2%
Identity: 27%
Fold: RuvA C-terminal domain-like
Superfamily: Hypothetical protein AF0491, middle domain
Family: Hypothetical protein AF0491, middle domain

Phyre2
16 |
| d1fcqa_ |

### PDB 1fcq chain A

Region: 42 - 95
Aligned: 49
Modelled: 54
Confidence: 9.4%
Identity: 22%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: Bee venom hyaluronidase

Phyre2
17 |
| c1fcuA_ |

### PDB 1fcu chain A

Region: 42 - 95
Aligned: 49
Modelled: 54
Confidence: 9.3%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:hyaluronoglucosaminidase;
PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase

Phyre2
18 |
| c3eabD_ |

### PDB 3eab chain D

Region: 52 - 64
Aligned: 13
Modelled: 13
Confidence: 8.6%
Identity: 38%
PDB header:cell cycle
Chain: D: PDB Molecule:spastin;
PDBTitle: crystal structure of spastin mit in complex with escrt iii

Phyre2
19 |
| c2z02A_ |

### PDB 2z02 chain A

Region: 36 - 76
Aligned: 41
Modelled: 41
Confidence: 7.8%
Identity: 29%
PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide
PDBTitle: crystal structure of2 phosphoribosylaminoimidazolesuccinocarboxamide synthase3 wit atp from methanocaldococcus jannaschii

Phyre2
20 |
| d1bh9b_ |

### PDB 1bh9 chain B

Region: 45 - 63
Aligned: 19
Modelled: 19
Confidence: 7.5%
Identity: 26%
Fold: Histone-fold
Superfamily: Histone-fold
Family: TBP-associated factors, TAFs

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2kmfA_ |
|  | 30.8 | 25 | PDB header:photosynthesis Chain: A: PDB Molecule:photosystem ii 11 kda protein; PDBTitle: solution structure of psb27 from cyanobacterial photosystem2 ii
2 | c2vdaB_ |
|  | 27.7 | 36 | PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex
3 | d1w6ua_ |
|  | 21.8 | 22 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases
4 | c1p5lA_ |
|  | 21.4 | 54 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution phe5 to ser modification in sds-d252 micelles
5 | c1p5kA_ |
|  | 20.0 | 54 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution ser to leu11 modification in sds-d252 micelles
6 | d1txka2 |
|  | 14.3 | 50 | Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:MdoG-like
7 | c1txkA_ |
|  | 13.2 | 50 | PDB header:biosynthetic protein Chain: A: PDB Molecule:glucans biosynthesis protein g; PDBTitle: crystal structure of escherichia coli opgg
8 | c1p0oA_ |
|  | 13.0 | 54 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution of trp for gln and asp at position2 17 and 19 modification in sds-d25 micelles
9 | c1p0jA_ |
|  | 12.9 | 54 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution asp to trp modification in sds-d252 micelles
10 | c1ot0A_ |
|  | 12.9 | 54 | PDB header:antibiotic Chain: A: PDB Molecule:50s ribosomal protein l1; PDBTitle: structure of antimicrobial peptide, hp (2-20) and its2 analogues derived from helicobacter pylori, as determined3 by 1h nmr spectroscopy
11 | c1p0lA_ |
|  | 12.7 | 54 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution gln to trp modification in sds-d252 micelles
12 | c1p0gA_ |
|  | 12.6 | 54 | PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: structure of antimicrobial peptide, hp (2-20) and its2 analogues derived from helicobacter pylori, as determined3 by 1h nmr spectroscopy
13 | c3gwnA_ |
|  | 12.6 | 17 | PDB header:oxidoreductase Chain: A: PDB Molecule:probable fad-linked sulfhydryl oxidase r596; PDBTitle: crystal structure of the fad binding domain from mimivirus sulfhydryl2 oxidase r596
14 | c2yytA_ |
|  | 12.0 | 21 | PDB header:lyase Chain: A: PDB Molecule:orotidine 5'-phosphate decarboxylase; PDBTitle: crystal structure of uncharacterized conserved protein from2 geobacillus kaustophilus
15 | d1t95a1 |
|  | 10.2 | 27 | Fold:RuvA C-terminal domain-like Superfamily:Hypothetical protein AF0491, middle domain Family:Hypothetical protein AF0491, middle domain
16 | d1fcqa_ |
|  | 9.4 | 22 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Bee venom hyaluronidase
17 | c1fcuA_ |
|  | 9.3 | 22 | PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase
18 | c3eabD_ |
|  | 8.6 | 38 | PDB header:cell cycle Chain: D: PDB Molecule:spastin; PDBTitle: crystal structure of spastin mit in complex with escrt iii
19 | c2z02A_ |
|  | 7.8 | 29 | PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide PDBTitle: crystal structure of2 phosphoribosylaminoimidazolesuccinocarboxamide synthase3 wit atp from methanocaldococcus jannaschii
20 | d1bh9b_ |
|  | 7.5 | 26 | Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs
21 | c2h31A_ |
| not modelled | 7.0 | 22 | PDB header:ligase, lyase Chain: A: PDB Molecule:multifunctional protein ade2; PDBTitle: crystal structure of human paics, a bifunctional carboxylase and2 synthetase in purine biosynthesis
22 | c2dl1A_ |
| not modelled | 6.3 | 22 | PDB header:protein transport Chain: A: PDB Molecule:spartin; PDBTitle: solution structure of the mit domain from human spartin
23 | d1cjca1 |
| not modelled | 5.9 | 12 | Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:C-terminal domain of adrenodoxin reductase-like
24 | c3kreA_ |
| not modelled | 5.5 | 17 | PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase; PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from ehrlichia chaffeensis at 1.8a resolution
25 | d1bf2a2 |
| not modelled | 5.4 | 14 | Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain
26 | c2x3bB_ |
| not modelled | 5.1 | 27 | PDB header:hydrolase Chain: B: PDB Molecule:toxic extracellular endopeptidase; PDBTitle: asap1 inactive mutant e294a, an extracellular toxic zinc2 metalloendopeptidase

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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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