Phyre 2 Results for P0AEN8

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Email | l.a.kelley@imperial.ac.uk
Description | P0AEN8
Date | Thu Jan 5 11:23:48 GMT 2012
Unique Job ID | d9e31f5a62f9b50a

Summary |

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

Model (left) based on template c2wcvI_
Top template information
PDB header:isomerase Chain: I: PDB Molecule:l-fucose mutarotase; PDBTitle: crystal structure of bacterial fucu
Confidence and coverage
Confidence: | 100.0% | Coverage: | 100%
140 residues (100% 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 | L | K | T | I | S | P | L | I | S | P | E | L | L | K | V | L | A | E | M | G | H | G | D | E | I | I | F | S | D | A | H | F | P | A | H | S | M | G | P | Q | V | I | R | A | D | G | L | L | V | S | D | L | L | Q | A | I | I | P | L
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SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
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Sequence |  | F | E | L | D | S | Y | A | P | P | L | V | M | M | A | A | V | E | G | D | T | L | D | P | E | V | E | R | R | Y | R | N | A | L | S | L | Q | A | P | C | P | D | I | I | R | I | N | R | F | A | F | Y | E | R | A | Q | K | A | F | A | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140
Sequence |  | V | I | T | G | E | R | A | K | Y | G | N | I | L | L | K | K | G | V | 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 |
| c2wcvI_ |

### PDB 2wcv chain I

Region: 1 - 140
Aligned: 140
Modelled: 140
Confidence: 100.0%
Identity: 100%
PDB header:isomerase
Chain: I: PDB Molecule:l-fucose mutarotase;
PDBTitle: crystal structure of bacterial fucu

Phyre2
2 |
| d2ob5a1 |

### PDB 2ob5 chain A domain 1

Region: 1 - 140
Aligned: 140
Modelled: 139
Confidence: 100.0%
Identity: 33%
Fold: RbsD-like
Superfamily: RbsD-like
Family: RbsD-like

Phyre2
3 |
| c2wcuB_ |

### PDB 2wcu chain B

Region: 2 - 139
Aligned: 138
Modelled: 138
Confidence: 100.0%
Identity: 47%
PDB header:isomerase
Chain: B: PDB Molecule:protein fucu homolog;
PDBTitle: crystal structure of mammalian fucu

Phyre2
4 |
| c3mvkA_ |

### PDB 3mvk chain A

Region: 5 - 139
Aligned: 135
Modelled: 134
Confidence: 100.0%
Identity: 41%
PDB header:isomerase
Chain: A: PDB Molecule:protein fucu;
PDBTitle: the crystal structure of fucu from bifidobacterium longum to 1.65a

Phyre2
5 |
| c3e7nB_ |

### PDB 3e7n chain B

Region: 2 - 139
Aligned: 135
Modelled: 138
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: B: PDB Molecule:d-ribose high-affinity transport system;
PDBTitle: crystal structure of d-ribose high-affinity transport system from2 salmonella typhimurium lt2

Phyre2
6 |
| d1ogda_ |

### PDB 1ogd chain A

Region: 1 - 139
Aligned: 130
Modelled: 139
Confidence: 100.0%
Identity: 21%
Fold: RbsD-like
Superfamily: RbsD-like
Family: RbsD-like

Phyre2
7 |
| c3p13B_ |

### PDB 3p13 chain B

Region: 7 - 139
Aligned: 129
Modelled: 133
Confidence: 100.0%
Identity: 16%
PDB header:isomerase
Chain: B: PDB Molecule:d-ribose pyranase;
PDBTitle: complex structure of d-ribose pyranase sa240 with d-ribose

Phyre2
8 |
| d1qkia1 |

### PDB 1qki chain A domain 1

Region: 51 - 119
Aligned: 65
Modelled: 69
Confidence: 26.7%
Identity: 15%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Phyre2
9 |
| c1e1cA_ |

### PDB 1e1c chain A

Region: 11 - 64
Aligned: 54
Modelled: 54
Confidence: 22.2%
Identity: 20%
PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant

Phyre2
10 |
| d1e3da_ |

### PDB 1e3d chain A

Region: 108 - 132
Aligned: 25
Modelled: 25
Confidence: 18.9%
Identity: 36%
Fold: HydA/Nqo6-like
Superfamily: HydA/Nqo6-like
Family: Nickel-iron hydrogenase, small subunit

Phyre2
11 |
| c2dgbA_ |

### PDB 2dgb chain A

Region: 1 - 23
Aligned: 21
Modelled: 23
Confidence: 17.6%
Identity: 33%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein purs;
PDBTitle: structure of thermus thermophilus purs in the p21 form

Phyre2
12 |
| d1t4aa_ |

### PDB 1t4a chain A

Region: 1 - 24
Aligned: 22
Modelled: 24
Confidence: 16.3%
Identity: 18%
Fold: PurS-like
Superfamily: PurS-like
Family: PurS subunit of FGAM synthetase

Phyre2
13 |
| d1frfs_ |

### PDB 1frf chain S

Region: 108 - 132
Aligned: 25
Modelled: 25
Confidence: 15.4%
Identity: 28%
Fold: HydA/Nqo6-like
Superfamily: HydA/Nqo6-like
Family: Nickel-iron hydrogenase, small subunit

Phyre2
14 |
| d1cc1s_ |

### PDB 1cc1 chain S

Region: 108 - 132
Aligned: 25
Modelled: 25
Confidence: 15.1%
Identity: 32%
Fold: HydA/Nqo6-like
Superfamily: HydA/Nqo6-like
Family: Nickel-iron hydrogenase, small subunit

Phyre2
15 |
| c2yx5A_ |

### PDB 2yx5 chain A

Region: 1 - 24
Aligned: 22
Modelled: 24
Confidence: 14.4%
Identity: 27%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0062 protein mj1593;
PDBTitle: crystal structure of methanocaldococcus jannaschii purs, one of the2 subunits of formylglycinamide ribonucleotide amidotransferase in the3 purine biosynthetic pathway

Phyre2
16 |
| c3myrE_ |

### PDB 3myr chain E

Region: 108 - 132
Aligned: 25
Modelled: 25
Confidence: 14.0%
Identity: 24%
PDB header:oxidoreductase
Chain: E: PDB Molecule:hydrogenase (nife) small subunit hyda;
PDBTitle: crystal structure of [nife] hydrogenase from allochromatium vinosum in2 its ni-a state

Phyre2
17 |
| d1wuis1 |

### PDB 1wui chain S domain 1

Region: 108 - 132
Aligned: 25
Modelled: 25
Confidence: 13.8%
Identity: 24%
Fold: HydA/Nqo6-like
Superfamily: HydA/Nqo6-like
Family: Nickel-iron hydrogenase, small subunit

Phyre2
18 |
| c1h2aS_ |

### PDB 1h2a chain S

Region: 108 - 132
Aligned: 25
Modelled: 25
Confidence: 13.7%
Identity: 24%
PDB header:oxidoreductase
Chain: S: PDB Molecule:hydrogenase;
PDBTitle: single crystals of hydrogenase from desulfovibrio vulgaris

Phyre2
19 |
| c3iymA_ |

### PDB 3iym chain A

Region: 60 - 110
Aligned: 50
Modelled: 51
Confidence: 13.0%
Identity: 24%
PDB header:virus
Chain: A: PDB Molecule:capsid protein;
PDBTitle: backbone trace of the capsid protein dimer of a fungal partitivirus2 from electron cryomicroscopy and homology modeling

Phyre2
20 |
| d1guza1 |

### PDB 1guz chain A domain 1

Region: 13 - 32
Aligned: 20
Modelled: 20
Confidence: 11.4%
Identity: 25%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: LDH N-terminal domain-like

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2wcvI_ |
|  | 100.0 | 100 | PDB header:isomerase Chain: I: PDB Molecule:l-fucose mutarotase; PDBTitle: crystal structure of bacterial fucu
2 | d2ob5a1 |
|  | 100.0 | 33 | Fold:RbsD-like Superfamily:RbsD-like Family:RbsD-like
3 | c2wcuB_ |
|  | 100.0 | 47 | PDB header:isomerase Chain: B: PDB Molecule:protein fucu homolog; PDBTitle: crystal structure of mammalian fucu
4 | c3mvkA_ |
|  | 100.0 | 41 | PDB header:isomerase Chain: A: PDB Molecule:protein fucu; PDBTitle: the crystal structure of fucu from bifidobacterium longum to 1.65a
5 | c3e7nB_ |
|  | 100.0 | 18 | PDB header:transport protein Chain: B: PDB Molecule:d-ribose high-affinity transport system; PDBTitle: crystal structure of d-ribose high-affinity transport system from2 salmonella typhimurium lt2
6 | d1ogda_ |
|  | 100.0 | 21 | Fold:RbsD-like Superfamily:RbsD-like Family:RbsD-like
7 | c3p13B_ |
|  | 100.0 | 16 | PDB header:isomerase Chain: B: PDB Molecule:d-ribose pyranase; PDBTitle: complex structure of d-ribose pyranase sa240 with d-ribose
8 | d1qkia1 |
|  | 26.7 | 15 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
9 | c1e1cA_ |
|  | 22.2 | 20 | PDB header:isomerase Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain; PDBTitle: methylmalonyl-coa mutase h244a mutant
10 | d1e3da_ |
|  | 18.9 | 36 | Fold:HydA/Nqo6-like Superfamily:HydA/Nqo6-like Family:Nickel-iron hydrogenase, small subunit
11 | c2dgbA_ |
|  | 17.6 | 33 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein purs; PDBTitle: structure of thermus thermophilus purs in the p21 form
12 | d1t4aa_ |
|  | 16.3 | 18 | Fold:PurS-like Superfamily:PurS-like Family:PurS subunit of FGAM synthetase
13 | d1frfs_ |
|  | 15.4 | 28 | Fold:HydA/Nqo6-like Superfamily:HydA/Nqo6-like Family:Nickel-iron hydrogenase, small subunit
14 | d1cc1s_ |
|  | 15.1 | 32 | Fold:HydA/Nqo6-like Superfamily:HydA/Nqo6-like Family:Nickel-iron hydrogenase, small subunit
15 | c2yx5A_ |
|  | 14.4 | 27 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0062 protein mj1593; PDBTitle: crystal structure of methanocaldococcus jannaschii purs, one of the2 subunits of formylglycinamide ribonucleotide amidotransferase in the3 purine biosynthetic pathway
16 | c3myrE_ |
|  | 14.0 | 24 | PDB header:oxidoreductase Chain: E: PDB Molecule:hydrogenase (nife) small subunit hyda; PDBTitle: crystal structure of [nife] hydrogenase from allochromatium vinosum in2 its ni-a state
17 | d1wuis1 |
|  | 13.8 | 24 | Fold:HydA/Nqo6-like Superfamily:HydA/Nqo6-like Family:Nickel-iron hydrogenase, small subunit
18 | c1h2aS_ |
|  | 13.7 | 24 | PDB header:oxidoreductase Chain: S: PDB Molecule:hydrogenase; PDBTitle: single crystals of hydrogenase from desulfovibrio vulgaris
19 | c3iymA_ |
|  | 13.0 | 24 | PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: backbone trace of the capsid protein dimer of a fungal partitivirus2 from electron cryomicroscopy and homology modeling
20 | d1guza1 |
|  | 11.4 | 25 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like
21 | d1gtda_ |
| not modelled | 10.8 | 35 | Fold:PurS-like Superfamily:PurS-like Family:PurS subunit of FGAM synthetase
22 | d176la_ |
| not modelled | 10.7 | 27 | Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme
23 | c3rgwS_ |
| not modelled | 10.3 | 28 | PDB header:oxidoreductase/oxidoreductase Chain: S: PDB Molecule:membrane-bound hydrogenase (nife) small subunit hoxk; PDBTitle: crystal structure at 1.5 a resolution of an h2-reduced, o2-tolerant2 hydrogenase from ralstonia eutropha unmasks a novel iron-sulfur3 cluster
24 | c2wpnA_ |
| not modelled | 10.1 | 36 | PDB header:oxidoreductase Chain: A: PDB Molecule:periplasmic [nifese] hydrogenase, small subunit; PDBTitle: structure of the oxidised, as-isolated nifese hydrogenase2 from d. vulgaris hildenborough
25 | d5ldha1 |
| not modelled | 9.6 | 14 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like
26 | d1yq9a1 |
| not modelled | 8.8 | 35 | Fold:HydA/Nqo6-like Superfamily:HydA/Nqo6-like Family:Nickel-iron hydrogenase, small subunit
27 | d1vs6z1 |
| not modelled | 8.0 | 36 | Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L31p
28 | d1llda1 |
| not modelled | 8.0 | 30 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like
29 | c1w1wF_ |
| not modelled | 7.7 | 20 | PDB header:cell adhesion Chain: F: PDB Molecule:sister chromatid cohesion protein 1; PDBTitle: sc smc1hd:scc1-c complex, atpgs
30 | d1w1we_ |
| not modelled | 7.7 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Rad21/Rec8-like
31 | d1vpka2 |
| not modelled | 7.7 | 9 | Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase III, beta subunit
32 | d189la_ |
| not modelled | 7.6 | 27 | Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme
33 | d1ldna1 |
| not modelled | 6.9 | 35 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like
34 | d1p37a_ |
| not modelled | 6.9 | 27 | Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme
35 | d2ldxa1 |
| not modelled | 6.7 | 25 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like
36 | d1swya_ |
| not modelled | 6.4 | 27 | Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme
37 | d1yjma1 |
| not modelled | 6.2 | 23 | Fold:SMAD/FHA domain Superfamily:SMAD/FHA domain Family:FHA domain
38 | d1gpma3 |
| not modelled | 5.9 | 30 | Fold:Alpha-lytic protease prodomain-like Superfamily:GMP synthetase C-terminal dimerisation domain Family:GMP synthetase C-terminal dimerisation domain
39 | d1hyha1 |
| not modelled | 5.9 | 30 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like
40 | d1vq3a_ |
| not modelled | 5.8 | 27 | Fold:PurS-like Superfamily:PurS-like Family:PurS subunit of FGAM synthetase
41 | d1cp2a_ |
| not modelled | 5.8 | 26 | Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like
42 | c2b664_ |
| not modelled | 5.6 | 36 | PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: 50s ribosomal subunit from a crystal structure of release factor rf1,2 trnas and mrna bound to the ribosome. this file contains the 50s3 subunit from a crystal structure of release factor rf1, trnas and4 mrna bound to the ribosome and is described in remark 400
43 | c2xd4A_ |
| not modelled | 5.6 | 9 | PDB header:ligase Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase; PDBTitle: nucleotide-bound structures of bacillus subtilis glycinamide2 ribonucleotide synthetase
44 | d1jkea_ |
| not modelled | 5.5 | 25 | Fold:DTD-like Superfamily:DTD-like Family:DTD-like
45 | c1yj5C_ |
| not modelled | 5.5 | 23 | PDB header:transferase Chain: C: PDB Molecule:5' polynucleotide kinase-3' phosphatase fha domain; PDBTitle: molecular architecture of mammalian polynucleotide kinase, a dna2 repair enzyme
46 | d1llca1 |
| not modelled | 5.5 | 20 | Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like
47 | c2zw2B_ |
| not modelled | 5.4 | 18 | PDB header:ligase Chain: B: PDB Molecule:putative uncharacterized protein sts178; PDBTitle: crystal structure of formylglycinamide ribonucleotide amidotransferase2 iii from sulfolobus tokodaii (stpurs)
48 | c3hl4B_ |
| not modelled | 5.2 | 10 | PDB header:transferase Chain: B: PDB Molecule:choline-phosphate cytidylyltransferase a; PDBTitle: crystal structure of a mammalian ctp:phosphocholine2 cytidylyltransferase with cdp-choline
49 | c2j034_ |
| not modelled | 5.1 | 36 | PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: structure of the thermus thermophilus 70s ribosome2 complexed with mrna, trna and paromomycin (part 4 of 4).3 this file contains the 50s subunit from molecule ii.

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