Phyre 2 Results for P0ABU9

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Email | l.a.kelley@imperial.ac.uk
Description | P0ABU9
Date | Thu Jan 5 11:16:27 GMT 2012
Unique Job ID | dc1f38dbb00d2a73

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2bbjB_
Top template information
PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter
Confidence and coverage
Confidence: | 79.2% | Coverage: | 47%
107 residues ( 47% of your sequence) have been modelled with 79.2% 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 | T | D | M | N | I | L | D | L | F | L | K | A | S | L | L | V | K | L | I | M | L | I | L | I | G | F | S | I | A | S | W | A | I | I | I | Q | R | T | R | I | L | N | A | A | A | R | E | A | E | A | F | E | D | K | F | W | S | G | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | E | L | S | R | L | Y | Q | E | S | Q | G | K | R | D | N | L | T | G | S | E | Q | I | F | Y | S | G | F | K | E | F | V | R | L | H | R | A | N | S | H | A | P | E | A | V | V | E | G | A | S | R | A | M | R | I | S | M | N | R | E | L
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  | ? | ? |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | E | N | L | E | T | H | I | P | F | L | G | T | V | G | S | I | S | P | Y | I | G | L | F | G | T | V | W | G | I | M | H | A | F | I | A | L | G | A | V | K | Q | A | T | L | Q | M | V | A | P | G | I | A | E | A | L | I | A | T | A | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230
Sequence |  | G | L | F | A | A | I | P | A | V | M | A | Y | N | R | L | N | Q | R | V | N | K | L | E | L | N | Y | D | N | F | M | E | E | F | T | A | I | L | H | R | Q | A | F | T | V | S | E | S | N | K | G
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 |
| c2bbjB_ |

### PDB 2bbj chain B

Region: 35 - 149
Aligned: 107
Modelled: 115
Confidence: 79.2%
Identity: 15%
PDB header:metal transport/membrane protein
Chain: B: PDB Molecule:divalent cation transport-related protein;
PDBTitle: crystal structure of the cora mg2+ transporter

Phyre2
2 |
| c1ciiA_ |

### PDB 1cii chain A

Region: 113 - 205
Aligned: 93
Modelled: 93
Confidence: 66.3%
Identity: 13%
PDB header:transmembrane protein
Chain: A: PDB Molecule:colicin ia;
PDBTitle: colicin ia

Phyre2
3 |
| d1o5ha_ |

### PDB 1o5h chain A

Region: 159 - 219
Aligned: 58
Modelled: 61
Confidence: 26.4%
Identity: 9%
Fold: Methenyltetrahydrofolate cyclohydrolase-like
Superfamily: Methenyltetrahydrofolate cyclohydrolase-like
Family: Methenyltetrahydrofolate cyclohydrolase-like

Phyre2
4 |
| c2ap7A_ |

### PDB 2ap7 chain A

Region: 136 - 148
Aligned: 13
Modelled: 13
Confidence: 25.8%
Identity: 46%
PDB header:antibiotic
Chain: A: PDB Molecule:bombinin h2;
PDBTitle: solution structure of bombinin h2 in dpc micelles

Phyre2
5 |
| c2ap8A_ |

### PDB 2ap8 chain A

Region: 136 - 148
Aligned: 13
Modelled: 13
Confidence: 23.8%
Identity: 46%
PDB header:antibiotic
Chain: A: PDB Molecule:bombinin h4;
PDBTitle: solution structure of bombinin h4 in dpc micelles

Phyre2
6 |
| d1jt6a1 |

### PDB 1jt6 chain A domain 1

Region: 169 - 223
Aligned: 51
Modelled: 55
Confidence: 20.9%
Identity: 6%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2
7 |
| d1rkta1 |

### PDB 1rkt chain A domain 1

Region: 169 - 224
Aligned: 52
Modelled: 56
Confidence: 16.0%
Identity: 10%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2
8 |
| c1tt9B_ |

### PDB 1tt9 chain B

Region: 160 - 219
Aligned: 57
Modelled: 57
Confidence: 15.3%
Identity: 9%
PDB header:transferase, lyase
Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase
PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer

Phyre2
9 |
| d1vi0a1 |

### PDB 1vi0 chain A domain 1

Region: 169 - 225
Aligned: 53
Modelled: 57
Confidence: 13.7%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2
10 |
| d1q8da_ |

### PDB 1q8d chain A

Region: 139 - 147
Aligned: 9
Modelled: 8
Confidence: 8.8%
Identity: 67%
Fold: GDNF receptor-like
Superfamily: GDNF receptor-like
Family: GDNF receptor-like

Phyre2
11 |
| c2dg8D_ |

### PDB 2dg8 chain D

Region: 169 - 226
Aligned: 54
Modelled: 58
Confidence: 8.1%
Identity: 11%
PDB header:gene regulation
Chain: D: PDB Molecule:putative tetr-family transcriptional regulatory protein;
PDBTitle: crystal structure of the putative trasncriptional regulator sco75182 from streptomyces coelicolor a3(2)

Phyre2
12 |
| d1zk8a1 |

### PDB 1zk8 chain A domain 1

Region: 169 - 222
Aligned: 50
Modelled: 54
Confidence: 8.1%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2
13 |
| d1pb6a1 |

### PDB 1pb6 chain A domain 1

Region: 169 - 219
Aligned: 47
Modelled: 51
Confidence: 7.5%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2
14 |
| c3s5rA_ |

### PDB 3s5r chain A

Region: 169 - 227
Aligned: 55
Modelled: 59
Confidence: 7.5%
Identity: 15%
PDB header:dna binding protein
Chain: A: PDB Molecule:transcriptional regulator tetr family;
PDBTitle: crystal structure of a putative transcriptional regulator of the tetr2 family (syn_02108) from syntrophus aciditrophicus at 2.60 a3 resolution

Phyre2
15 |
| d2fbqa1 |

### PDB 2fbq chain A domain 1

Region: 169 - 227
Aligned: 55
Modelled: 59
Confidence: 7.0%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Tetracyclin repressor-like, N-terminal domain

Phyre2
16 |
| c3gziA_ |

### PDB 3gzi chain A

Region: 170 - 228
Aligned: 55
Modelled: 59
Confidence: 6.9%
Identity: 11%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of a transcriptional regulator of the tetr family2 (shew_3567) from shewanella loihica pv-4 at 2.05 a resolution

Phyre2
17 |
| c2l4gA_ |

### PDB 2l4g chain A

Region: 141 - 151
Aligned: 11
Modelled: 11
Confidence: 6.7%
Identity: 45%
PDB header:viral protein
Chain: A: PDB Molecule:haemagglutinin;
PDBTitle: influenza haemagglutinin fusion peptide mutant g13a

Phyre2
18 |
| c1u9nA_ |

### PDB 1u9n chain A

Region: 169 - 228
Aligned: 56
Modelled: 60
Confidence: 6.4%
Identity: 16%
PDB header:dna binding protein
Chain: A: PDB Molecule:transcriptional repressor ethr;
PDBTitle: crystal structure of the transcriptional regulator ethr in2 a ligand bound conformation opens therapeutic perspectives3 against tuberculosis and leprosy

Phyre2
19 |
| c2v5eA_ |

### PDB 2v5e chain A

Region: 136 - 147
Aligned: 12
Modelled: 12
Confidence: 6.2%
Identity: 50%
PDB header:receptor/glycoprotein complex
Chain: A: PDB Molecule:gdnf family receptor alpha-1;
PDBTitle: the structure of the gdnf\:coreceptor complex\: insights2 into ret signalling and heparin binding.

Phyre2
20 |
| c3fubA_ |

### PDB 3fub chain A

Region: 136 - 147
Aligned: 12
Modelled: 12
Confidence: 6.2%
Identity: 50%
PDB header:hormone
Chain: A: PDB Molecule:gdnf family receptor alpha-1;
PDBTitle: crystal structure of gdnf-gfralpha1 complex

Phyre2
21 |
22 |
23 |
24 |
25 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2bbjB_ |
|  | 79.2 | 15 | PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter
2 | c1ciiA_ |
|  | 66.3 | 13 | PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia
3 | d1o5ha_ |
|  | 26.4 | 9 | Fold:Methenyltetrahydrofolate cyclohydrolase-like Superfamily:Methenyltetrahydrofolate cyclohydrolase-like Family:Methenyltetrahydrofolate cyclohydrolase-like
4 | c2ap7A_ |
|  | 25.8 | 46 | PDB header:antibiotic Chain: A: PDB Molecule:bombinin h2; PDBTitle: solution structure of bombinin h2 in dpc micelles
5 | c2ap8A_ |
|  | 23.8 | 46 | PDB header:antibiotic Chain: A: PDB Molecule:bombinin h4; PDBTitle: solution structure of bombinin h4 in dpc micelles
6 | d1jt6a1 |
|  | 20.9 | 6 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
7 | d1rkta1 |
|  | 16.0 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
8 | c1tt9B_ |
|  | 15.3 | 9 | PDB header:transferase, lyase Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer
9 | d1vi0a1 |
|  | 13.7 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
10 | d1q8da_ |
|  | 8.8 | 67 | Fold:GDNF receptor-like Superfamily:GDNF receptor-like Family:GDNF receptor-like
11 | c2dg8D_ |
|  | 8.1 | 11 | PDB header:gene regulation Chain: D: PDB Molecule:putative tetr-family transcriptional regulatory protein; PDBTitle: crystal structure of the putative trasncriptional regulator sco75182 from streptomyces coelicolor a3(2)
12 | d1zk8a1 |
|  | 8.1 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
13 | d1pb6a1 |
|  | 7.5 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
14 | c3s5rA_ |
|  | 7.5 | 15 | PDB header:dna binding protein Chain: A: PDB Molecule:transcriptional regulator tetr family; PDBTitle: crystal structure of a putative transcriptional regulator of the tetr2 family (syn_02108) from syntrophus aciditrophicus at 2.60 a3 resolution
15 | d2fbqa1 |
|  | 7.0 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
16 | c3gziA_ |
|  | 6.9 | 11 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: crystal structure of a transcriptional regulator of the tetr family2 (shew_3567) from shewanella loihica pv-4 at 2.05 a resolution
17 | c2l4gA_ |
|  | 6.7 | 45 | PDB header:viral protein Chain: A: PDB Molecule:haemagglutinin; PDBTitle: influenza haemagglutinin fusion peptide mutant g13a
18 | c1u9nA_ |
|  | 6.4 | 16 | PDB header:dna binding protein Chain: A: PDB Molecule:transcriptional repressor ethr; PDBTitle: crystal structure of the transcriptional regulator ethr in2 a ligand bound conformation opens therapeutic perspectives3 against tuberculosis and leprosy
19 | c2v5eA_ |
|  | 6.2 | 50 | PDB header:receptor/glycoprotein complex Chain: A: PDB Molecule:gdnf family receptor alpha-1; PDBTitle: the structure of the gdnf\:coreceptor complex\: insights2 into ret signalling and heparin binding.
20 | c3fubA_ |
|  | 6.2 | 50 | PDB header:hormone Chain: A: PDB Molecule:gdnf family receptor alpha-1; PDBTitle: crystal structure of gdnf-gfralpha1 complex
21 | c2dciA_ |
| not modelled | 6.2 | 45 | PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of influenza ha fusion peptide mutant w14a in2 dpc in ph5
22 | c2oerA_ |
| not modelled | 5.7 | 13 | PDB header:transcription Chain: A: PDB Molecule:probable transcriptional regulator; PDBTitle: probable transcriptional regulator from pseudomonas2 aeruginosa
23 | c2hjdA_ |
| not modelled | 5.4 | 12 | PDB header:signaling protein Chain: A: PDB Molecule:quorum-sensing antiactivator; PDBTitle: crystal structure of a second quorum sensing antiactivator tram2 from2 a. tumefaciens strain a6
24 | d2o7ta1 |
| not modelled | 5.3 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain
25 | c3eupA_ |
| not modelled | 5.1 | 11 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: the crystal structure of the transcriptional regulator, tetr family2 from cytophaga hutchinsonii

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

Transmembrane helix prediction |

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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