Phyre 2 Results for P62395

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Email | l.a.kelley@imperial.ac.uk
Description | P62395
Date | Thu Jan 5 12:07:29 GMT 2012
Unique Job ID | 0f3a5c7f0451b9f3

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3ibpA_
Top template information
PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: the crystal structure of the dimerization domain of escherichia coli2 structural maintenance of chromosomes protein mukb
Confidence and coverage
Confidence: | 24.8% | Coverage: | 19%
33 residues ( 19% of your sequence) have been modelled with 24.8% 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 | G | I | L | T | R | W | R | Q | F | G | K | R | Y | F | W | P | H | L | L | L | G | M | V | A | A | S | L | G | L | P | A | L | S | N | A | A | E | P | N | A | P | A | K | A | T | T | R | N | H | E | P | S | A | K | V | N | F | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | Q | L | A | L | L | E | A | N | T | R | R | P | N | S | N | Y | S | V | D | Y | W | H | Q | H | A | I | R | T | V | I | R | H | L | S | F | A | M | A | P | Q | T | L | P | V | A | E | E | S | L | P | L | Q | A | Q | H | L | A | L | L | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170
Sequence |  | T | L | S | A | L | L | T | Q | E | G | T | P | S | E | K | G | Y | R | I | D | Y | A | H | F | T | P | Q | A | K | F | S | T | P | V | W | I | S | Q | A | Q | G | I | R | A | G | P | Q | R | L | T
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 |
| c3ibpA_ |

### PDB 3ibp chain A

Region: 82 - 114
Aligned: 33
Modelled: 33
Confidence: 24.8%
Identity: 18%
PDB header:cell cycle
Chain: A: PDB Molecule:chromosome partition protein mukb;
PDBTitle: the crystal structure of the dimerization domain of escherichia coli2 structural maintenance of chromosomes protein mukb

Phyre2
2 |
| c3ostA_ |

### PDB 3ost chain A

Region: 4 - 12
Aligned: 9
Modelled: 9
Confidence: 20.8%
Identity: 44%
PDB header:lipid binding protein
Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4;
PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p

Phyre2
3 |
| d1wdka2 |

### PDB 1wdk chain A domain 2

Region: 4 - 30
Aligned: 27
Modelled: 27
Confidence: 12.8%
Identity: 15%
Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like
Family: HCDH C-domain-like

Phyre2
4 |
| c1jb0X_ |

### PDB 1jb0 chain X

Region: 14 - 24
Aligned: 11
Modelled: 11
Confidence: 12.4%
Identity: 55%
PDB header:photosynthesis
Chain: X: PDB Molecule:photosystem i subunit psax;
PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria

Phyre2
5 |
| d1jb0x_ |

### PDB 1jb0 chain X

Region: 14 - 24
Aligned: 11
Modelled: 11
Confidence: 12.4%
Identity: 55%
Fold: Single transmembrane helix
Superfamily: Subunit PsaX of photosystem I reaction centre
Family: Subunit PsaX of photosystem I reaction centre

Phyre2
6 |
| c3pcqX_ |

### PDB 3pcq chain X

Region: 14 - 24
Aligned: 11
Modelled: 11
Confidence: 11.6%
Identity: 55%
PDB header:photosynthesis
Chain: X: PDB Molecule:photosystem i 4.8k protein;
PDBTitle: femtosecond x-ray protein nanocrystallography

Phyre2
7 |
| d1zmba1 |

### PDB 1zmb chain A domain 1

Region: 9 - 17
Aligned: 9
Modelled: 9
Confidence: 11.0%
Identity: 67%
Fold: Flavodoxin-like
Superfamily: SGNH hydrolase
Family: Putative acetylxylan esterase-like

Phyre2
8 |
| d1ylea1 |

### PDB 1yle chain A domain 1

Region: 1 - 16
Aligned: 16
Modelled: 16
Confidence: 10.3%
Identity: 25%
Fold: Acyl-CoA N-acyltransferases (Nat)
Superfamily: Acyl-CoA N-acyltransferases (Nat)
Family: AstA-like

Phyre2
9 |
| c2ks1B_ |

### PDB 2ks1 chain B

Region: 20 - 31
Aligned: 12
Modelled: 12
Confidence: 9.5%
Identity: 58%
PDB header:transferase
Chain: B: PDB Molecule:epidermal growth factor receptor;
PDBTitle: heterodimeric association of transmembrane domains of erbb1 and erbb22 receptors enabling kinase activation

Phyre2
10 |
| d2fiqa1 |

### PDB 2fiq chain A domain 1

Region: 12 - 19
Aligned: 8
Modelled: 8
Confidence: 9.4%
Identity: 63%
Fold: TIM beta/alpha-barrel
Superfamily: Aldolase
Family: GatZ-like

Phyre2
11 |
| d2izva1 |

### PDB 2izv chain A domain 1

Region: 83 - 94
Aligned: 12
Modelled: 12
Confidence: 9.2%
Identity: 50%
Fold: SOCS box-like
Superfamily: SOCS box-like
Family: SOCS box-like

Phyre2
12 |
| c3nnqA_ |

### PDB 3nnq chain A

Region: 3 - 20
Aligned: 18
Modelled: 12
Confidence: 8.2%
Identity: 6%
PDB header:viral protein
Chain: A: PDB Molecule:n-terminal domain of moloney murine leukemia virus
PDBTitle: crystal structure of the n-terminal domain of moloney murine leukemia2 virus integrase, northeast structural genomics consortium target or3

Phyre2
13 |
| d1hlya_ |

### PDB 1hly chain A

Region: 161 - 165
Aligned: 5
Modelled: 5
Confidence: 7.9%
Identity: 100%
Fold: Knottins (small inhibitors, toxins, lectins)
Superfamily: Scorpion toxin-like
Family: Short-chain scorpion toxins

Phyre2
14 |
| d1g3nc2 |

### PDB 1g3n chain C domain 2

Region: 75 - 90
Aligned: 15
Modelled: 16
Confidence: 7.8%
Identity: 40%
Fold: Cyclin-like
Superfamily: Cyclin-like
Family: Cyclin

Phyre2
15 |
| d1vf5g_ |

### PDB 1vf5 chain G

Region: 20 - 30
Aligned: 11
Modelled: 11
Confidence: 7.0%
Identity: 64%
Fold: Single transmembrane helix
Superfamily: PetG subunit of the cytochrome b6f complex
Family: PetG subunit of the cytochrome b6f complex

Phyre2
16 |
| c1vf5G_ |

### PDB 1vf5 chain G

Region: 20 - 30
Aligned: 11
Modelled: 11
Confidence: 7.0%
Identity: 64%
PDB header:photosynthesis
Chain: G: PDB Molecule:protein pet g;
PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus

Phyre2
17 |
| d2e74g1 |

### PDB 2e74 chain G domain 1

Region: 20 - 30
Aligned: 11
Modelled: 11
Confidence: 6.9%
Identity: 64%
Fold: Single transmembrane helix
Superfamily: PetG subunit of the cytochrome b6f complex
Family: PetG subunit of the cytochrome b6f complex

Phyre2
18 |
| c2e76D_ |

### PDB 2e76 chain D

Region: 11 - 30
Aligned: 20
Modelled: 20
Confidence: 6.7%
Identity: 30%
PDB header:photosynthesis
Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit;
PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus

Phyre2
19 |
| c2qdoC_ |

### PDB 2qdo chain C

Region: 88 - 93
Aligned: 6
Modelled: 6
Confidence: 6.5%
Identity: 67%
PDB header:photosynthesis
Chain: C: PDB Molecule:nbla protein;
PDBTitle: nbla protein from t. vulcanus

Phyre2
20 |
| c3d7vB_ |

### PDB 3d7v chain B

Region: 151 - 158
Aligned: 8
Modelled: 8
Confidence: 6.2%
Identity: 38%
PDB header:apoptosis
Chain: B: PDB Molecule:bcl-2-like protein 11;
PDBTitle: crystal structure of mcl-1 in complex with an mcl-12 selective bh3 ligand

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3ibpA_ |
|  | 24.8 | 18 | PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: the crystal structure of the dimerization domain of escherichia coli2 structural maintenance of chromosomes protein mukb
2 | c3ostA_ |
|  | 20.8 | 44 | PDB header:lipid binding protein Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4; PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p
3 | d1wdka2 |
|  | 12.8 | 15 | Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:HCDH C-domain-like
4 | c1jb0X_ |
|  | 12.4 | 55 | PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i subunit psax; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria
5 | d1jb0x_ |
|  | 12.4 | 55 | Fold:Single transmembrane helix Superfamily:Subunit PsaX of photosystem I reaction centre Family:Subunit PsaX of photosystem I reaction centre
6 | c3pcqX_ |
|  | 11.6 | 55 | PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i 4.8k protein; PDBTitle: femtosecond x-ray protein nanocrystallography
7 | d1zmba1 |
|  | 11.0 | 67 | Fold:Flavodoxin-like Superfamily:SGNH hydrolase Family:Putative acetylxylan esterase-like
8 | d1ylea1 |
|  | 10.3 | 25 | Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:AstA-like
9 | c2ks1B_ |
|  | 9.5 | 58 | PDB header:transferase Chain: B: PDB Molecule:epidermal growth factor receptor; PDBTitle: heterodimeric association of transmembrane domains of erbb1 and erbb22 receptors enabling kinase activation
10 | d2fiqa1 |
|  | 9.4 | 63 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:GatZ-like
11 | d2izva1 |
|  | 9.2 | 50 | Fold:SOCS box-like Superfamily:SOCS box-like Family:SOCS box-like
12 | c3nnqA_ |
|  | 8.2 | 6 | PDB header:viral protein Chain: A: PDB Molecule:n-terminal domain of moloney murine leukemia virus PDBTitle: crystal structure of the n-terminal domain of moloney murine leukemia2 virus integrase, northeast structural genomics consortium target or3
13 | d1hlya_ |
|  | 7.9 | 100 | Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins
14 | d1g3nc2 |
|  | 7.8 | 40 | Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin
15 | d1vf5g_ |
|  | 7.0 | 64 | Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex
16 | c1vf5G_ |
|  | 7.0 | 64 | PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus
17 | d2e74g1 |
|  | 6.9 | 64 | Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex
18 | c2e76D_ |
|  | 6.7 | 30 | PDB header:photosynthesis Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus
19 | c2qdoC_ |
|  | 6.5 | 67 | PDB header:photosynthesis Chain: C: PDB Molecule:nbla protein; PDBTitle: nbla protein from t. vulcanus
20 | c3d7vB_ |
|  | 6.2 | 38 | PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: crystal structure of mcl-1 in complex with an mcl-12 selective bh3 ligand
21 | c2kfdA_ |
| not modelled | 6.1 | 50 | PDB header:nuclear protein Chain: A: PDB Molecule:pre-mrna-processing protein prp40; PDBTitle: prp40 ff4 domain
22 | c1bm4A_ |
| not modelled | 6.0 | 40 | PDB header:viral protein Chain: A: PDB Molecule:protein (moloney murine leukemia virus capsid); PDBTitle: momlv capsid protein major homology region peptide analog
23 | c2vy8A_ |
| not modelled | 6.0 | 43 | PDB header:transcription Chain: A: PDB Molecule:polymerase basic protein 2; PDBTitle: the 627-domain from influenza a virus polymerase pb22 subunit with glu-627
24 | c3io9B_ |
| not modelled | 6.0 | 38 | PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: biml12y in complex with mcl-1
25 | c3kj2B_ |
| not modelled | 6.0 | 38 | PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: mcl-1 in complex with bim bh3 mutant f4ae
26 | c2nl9B_ |
| not modelled | 5.9 | 38 | PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: crystal structure of the mcl-1:bim bh3 complex
27 | d2nysa1 |
| not modelled | 5.9 | 54 | Fold:SspB-like Superfamily:SspB-like Family:AGR C 3712p-like
28 | c2nysA_ |
| not modelled | 5.9 | 54 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:agr_c_3712p; PDBTitle: x-ray crystal structure of protein agr_c_3712 from2 agrobacterium tumefaciens. northeast structural genomics3 consortium target atr88.
29 | c3rfrI_ |
| not modelled | 5.6 | 35 | PDB header:oxidoreductase Chain: I: PDB Molecule:pmob; PDBTitle: crystal structure of particulate methane monooxygenase (pmmo) from2 methylocystis sp. strain m
30 | c2qazC_ |
| not modelled | 5.3 | 31 | PDB header:hydrolase activator Chain: C: PDB Molecule:sspb protein; PDBTitle: structure of c. crescentus sspb ortholog
31 | d2e74b1 |
| not modelled | 5.1 | 36 | Fold:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

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