Phyre 2 Results for P64562

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Email | l.a.kelley@imperial.ac.uk
Description | P64562
Date | Thu Jan 5 12:09:27 GMT 2012
Unique Job ID | 5d324b7380e48bcb

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c3hhfB_
Top template information
PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: structure of crga regulatory domain, a lysr-type transcriptional2 regulator from neisseria meningitidis.
Confidence and coverage
Confidence: | 99.3% | Coverage: | 95%
72 residues ( 95% of your sequence) have been modelled with 99.3% 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 | H | F | A | Q | R | V | R | A | L | V | V | L | N | G | V | A | L | L | P | Q | F | A | C | K | Q | G | L | A | N | G | E | L | V | R | L | F | A | P | W | S | G | I | P | R | P | L | Y | A | L | F | A | G | R | K | G | M | P | A | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | .
Sequence |  | A | R | Y | F | M | D | E | L | T | T | R | L | A | N | G | V
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 |
| c3hhfB_ |

### PDB 3hhf chain B

Region: 2 - 73
Aligned: 72
Modelled: 71
Confidence: 99.3%
Identity: 22%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, lysr family;
PDBTitle: structure of crga regulatory domain, a lysr-type transcriptional2 regulator from neisseria meningitidis.

Phyre2
2 |
| c3mz1D_ |

### PDB 3mz1 chain D

Region: 1 - 74
Aligned: 74
Modelled: 71
Confidence: 99.3%
Identity: 23%
PDB header:transcription regulator
Chain: D: PDB Molecule:putative transcriptional regulator;
PDBTitle: the crystal structure of a possible transcription regulator protein2 from sinorhizobium meliloti 1021

Phyre2
3 |
| c3t1bB_ |

### PDB 3t1b chain B

Region: 2 - 72
Aligned: 71
Modelled: 71
Confidence: 99.2%
Identity: 25%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, lysr family;
PDBTitle: crystal structure of the full-length aphb n100e variant

Phyre2
4 |
| c3kosA_ |

### PDB 3kos chain A

Region: 2 - 74
Aligned: 72
Modelled: 73
Confidence: 99.2%
Identity: 18%
PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional activator ampr;
PDBTitle: structure of the ampr effector binding domain from citrobacter2 freundii

Phyre2
5 |
| c3fd3A_ |

### PDB 3fd3 chain A

Region: 2 - 71
Aligned: 67
Modelled: 70
Confidence: 99.2%
Identity: 18%
PDB header:transcription regulator
Chain: A: PDB Molecule:chromosome replication initiation inhibitor protein;
PDBTitle: structure of the c-terminal domains of a lysr family protein from2 agrobacterium tumefaciens str. c58.

Phyre2
6 |
| c3hhgF_ |

### PDB 3hhg chain F

Region: 2 - 73
Aligned: 72
Modelled: 72
Confidence: 99.2%
Identity: 24%
PDB header:transcription regulator
Chain: F: PDB Molecule:transcriptional regulator, lysr family;
PDBTitle: structure of crga, a lysr-type transcriptional regulator from2 neisseria meningitidis.

Phyre2
7 |
| c2qsxB_ |

### PDB 2qsx chain B

Region: 1 - 73
Aligned: 73
Modelled: 73
Confidence: 99.2%
Identity: 21%
PDB header:transcription
Chain: B: PDB Molecule:putative transcriptional regulator, lysr family;
PDBTitle: crystal structure of putative transcriptional regulator lysr from2 vibrio parahaemolyticus

Phyre2
8 |
| c3fzjC_ |

### PDB 3fzj chain C

Region: 2 - 71
Aligned: 70
Modelled: 70
Confidence: 99.1%
Identity: 9%
PDB header:transcription regulator
Chain: C: PDB Molecule:lysr type regulator of tsambcd;
PDBTitle: tsar low resolution crystal structure, tetragonal form

Phyre2
9 |
| d1utha_ |

### PDB 1uth chain A

Region: 2 - 75
Aligned: 74
Modelled: 74
Confidence: 99.1%
Identity: 11%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
10 |
| c1al3A_ |

### PDB 1al3 chain A

Region: 2 - 73
Aligned: 71
Modelled: 72
Confidence: 99.0%
Identity: 14%
PDB header:transcription regulation
Chain: A: PDB Molecule:cys regulon transcriptional activator cysb;
PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes

Phyre2
11 |
| d1al3a_ |

### PDB 1al3 chain A

Region: 2 - 73
Aligned: 71
Modelled: 72
Confidence: 99.0%
Identity: 14%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
12 |
| c2uyeA_ |

### PDB 2uye chain A

Region: 2 - 75
Aligned: 74
Modelled: 74
Confidence: 99.0%
Identity: 11%
PDB header:transcription
Chain: A: PDB Molecule:regulatory protein;
PDBTitle: double mutant y110s,f111v dntr from burkholderia sp. strain2 dnt in complex with thiocyanate

Phyre2
13 |
| c3oxnD_ |

### PDB 3oxn chain D

Region: 2 - 74
Aligned: 73
Modelled: 73
Confidence: 99.0%
Identity: 11%
PDB header:transcription regulator
Chain: D: PDB Molecule:putative transcriptional regulator, lysr family;
PDBTitle: the crystal structure of a putative transcriptional regulator from2 vibrio parahaemolyticus

Phyre2
14 |
| c3fzvC_ |

### PDB 3fzv chain C

Region: 2 - 73
Aligned: 72
Modelled: 72
Confidence: 99.0%
Identity: 18%
PDB header:transcription regulator
Chain: C: PDB Molecule:probable transcriptional regulator;
PDBTitle: crystal structure of pa01 protein, putative lysr family2 transcriptional regulator from pseudomonas aeruginosa

Phyre2
15 |
| d1i6aa_ |

### PDB 1i6a chain A

Region: 2 - 74
Aligned: 73
Modelled: 73
Confidence: 98.9%
Identity: 14%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
16 |
| c2hxrA_ |

### PDB 2hxr chain A

Region: 2 - 73
Aligned: 69
Modelled: 72
Confidence: 98.9%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional regulator cynr;
PDBTitle: structure of the ligand binding domain of e. coli cynr, a2 transcriptional regulator controlling cyanate metabolism

Phyre2
17 |
| c3ispA_ |

### PDB 3isp chain A

Region: 2 - 74
Aligned: 69
Modelled: 73
Confidence: 98.9%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional regulator
PDBTitle: crystal structure of argp from mycobacterium tuberculosis

Phyre2
18 |
| c3jv9B_ |

### PDB 3jv9 chain B

Region: 2 - 76
Aligned: 74
Modelled: 75
Confidence: 98.9%
Identity: 9%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, lysr family;
PDBTitle: the structure of a reduced form of oxyr from n. meningitidis

Phyre2
19 |
| c1iz1B_ |

### PDB 1iz1 chain B

Region: 2 - 74
Aligned: 70
Modelled: 73
Confidence: 98.8%
Identity: 11%
PDB header:dna binding protein
Chain: B: PDB Molecule:lysr-type regulatory protein;
PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator

Phyre2
20 |
| c3n6uA_ |

### PDB 3n6u chain A

Region: 2 - 71
Aligned: 70
Modelled: 70
Confidence: 98.8%
Identity: 9%
PDB header:transcription regulator
Chain: A: PDB Molecule:lysr type regulator of tsambcd;
PDBTitle: effector binding domain of tsar in complex with its inducer p-2 toluenesulfonate

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3hhfB_ |
|  | 99.3 | 22 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: structure of crga regulatory domain, a lysr-type transcriptional2 regulator from neisseria meningitidis.
2 | c3mz1D_ |
|  | 99.3 | 23 | PDB header:transcription regulator Chain: D: PDB Molecule:putative transcriptional regulator; PDBTitle: the crystal structure of a possible transcription regulator protein2 from sinorhizobium meliloti 1021
3 | c3t1bB_ |
|  | 99.2 | 25 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: crystal structure of the full-length aphb n100e variant
4 | c3kosA_ |
|  | 99.2 | 18 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator ampr; PDBTitle: structure of the ampr effector binding domain from citrobacter2 freundii
5 | c3fd3A_ |
|  | 99.2 | 18 | PDB header:transcription regulator Chain: A: PDB Molecule:chromosome replication initiation inhibitor protein; PDBTitle: structure of the c-terminal domains of a lysr family protein from2 agrobacterium tumefaciens str. c58.
6 | c3hhgF_ |
|  | 99.2 | 24 | PDB header:transcription regulator Chain: F: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: structure of crga, a lysr-type transcriptional regulator from2 neisseria meningitidis.
7 | c2qsxB_ |
|  | 99.2 | 21 | PDB header:transcription Chain: B: PDB Molecule:putative transcriptional regulator, lysr family; PDBTitle: crystal structure of putative transcriptional regulator lysr from2 vibrio parahaemolyticus
8 | c3fzjC_ |
|  | 99.1 | 9 | PDB header:transcription regulator Chain: C: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: tsar low resolution crystal structure, tetragonal form
9 | d1utha_ |
|  | 99.1 | 11 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
10 | c1al3A_ |
|  | 99.0 | 14 | PDB header:transcription regulation Chain: A: PDB Molecule:cys regulon transcriptional activator cysb; PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes
11 | d1al3a_ |
|  | 99.0 | 14 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
12 | c2uyeA_ |
|  | 99.0 | 11 | PDB header:transcription Chain: A: PDB Molecule:regulatory protein; PDBTitle: double mutant y110s,f111v dntr from burkholderia sp. strain2 dnt in complex with thiocyanate
13 | c3oxnD_ |
|  | 99.0 | 11 | PDB header:transcription regulator Chain: D: PDB Molecule:putative transcriptional regulator, lysr family; PDBTitle: the crystal structure of a putative transcriptional regulator from2 vibrio parahaemolyticus
14 | c3fzvC_ |
|  | 99.0 | 18 | PDB header:transcription regulator Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: crystal structure of pa01 protein, putative lysr family2 transcriptional regulator from pseudomonas aeruginosa
15 | d1i6aa_ |
|  | 98.9 | 14 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
16 | c2hxrA_ |
|  | 98.9 | 16 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator cynr; PDBTitle: structure of the ligand binding domain of e. coli cynr, a2 transcriptional regulator controlling cyanate metabolism
17 | c3ispA_ |
|  | 98.9 | 16 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator PDBTitle: crystal structure of argp from mycobacterium tuberculosis
18 | c3jv9B_ |
|  | 98.9 | 9 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: the structure of a reduced form of oxyr from n. meningitidis
19 | c1iz1B_ |
|  | 98.8 | 11 | PDB header:dna binding protein Chain: B: PDB Molecule:lysr-type regulatory protein; PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator
20 | c3n6uA_ |
|  | 98.8 | 9 | PDB header:transcription regulator Chain: A: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: effector binding domain of tsar in complex with its inducer p-2 toluenesulfonate
21 | c2ql3G_ |
| not modelled | 98.8 | 17 | PDB header:transcription Chain: G: PDB Molecule:probable transcriptional regulator, lysr family protein; PDBTitle: crystal structure of the c-terminal domain of a probable lysr family2 transcriptional regulator from rhodococcus sp. rha1
22 | d2fyia1 |
| not modelled | 98.7 | 10 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
23 | c3ho7A_ |
| not modelled | 98.7 | 9 | PDB header:transcription Chain: A: PDB Molecule:oxyr; PDBTitle: crystal structure of oxyr from porphyromonas gingivalis
24 | c2h9qC_ |
| not modelled | 98.7 | 11 | PDB header:transcription Chain: C: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: crystal structure of the effector binding domain of a catm2 variant (r156h)
25 | d1ixca2 |
| not modelled | 98.6 | 11 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
26 | c2f7cA_ |
| not modelled | 98.5 | 11 | PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: catm effector binding domain with its effector cis,cis-muconate
27 | d2esna2 |
| not modelled | 98.5 | 13 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
28 | c2h9bB_ |
| not modelled | 98.4 | 14 | PDB header:transcription Chain: B: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of the effector binding domain of a benm variant2 (benm r156h/t157s)
29 | c2f78A_ |
| not modelled | 98.3 | 16 | PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: benm effector binding domain with its effector benzoate
30 | c2esnC_ |
| not modelled | 98.2 | 12 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: the crystal structure of probable transcriptional regulator pa04772 from pseudomonas aeruginosa
31 | c3onmB_ |
| not modelled | 97.3 | 10 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator lrha; PDBTitle: effector binding domain of lysr-type transcription factor rovm from y.2 pseudotuberculosis
32 | d1twya_ |
| not modelled | 50.5 | 7 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
33 | c1twyG_ |
| not modelled | 45.9 | 7 | PDB header:structural genomics, unknown function Chain: G: PDB Molecule:abc transporter, periplasmic substrate-binding protein; PDBTitle: crystal structure of an abc-type phosphate transport receptor from2 vibrio cholerae
34 | c3c5tB_ |
| not modelled | 41.9 | 30 | PDB header:signaling protein/signaling protein Chain: B: PDB Molecule:exendin-4; PDBTitle: crystal structure of the ligand-bound glucagon-like peptide-1 receptor2 extracellular domain
35 | c3lr1A_ |
| not modelled | 32.2 | 8 | PDB header:transport protein Chain: A: PDB Molecule:tungstate abc transporter, periplasmic tungstate- PDBTitle: the crystal structure of the tungstate abc transporter from2 geobacter sulfurreducens
36 | d1amfa_ |
| not modelled | 16.0 | 11 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
37 | c3muqB_ |
| not modelled | 14.9 | 15 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized conserved protein; PDBTitle: the crystal structure of a conserved functionally unknown protein from2 vibrio parahaemolyticus rimd 2210633
38 | d2i7xa1 |
| not modelled | 11.3 | 14 | Fold:Metallo-hydrolase/oxidoreductase Superfamily:Metallo-hydrolase/oxidoreductase Family:beta-CASP RNA-metabolising hydrolases
39 | c2i7xA_ |
| not modelled | 11.3 | 14 | PDB header:rna binding protein, protein binding Chain: A: PDB Molecule:protein cft2; PDBTitle: structure of yeast cpsf-100 (ydh1p)
40 | c1jrjA_ |
| not modelled | 11.1 | 18 | PDB header:hormone/growth factor Chain: A: PDB Molecule:exendin-4; PDBTitle: solution structure of exendin-4 in 30-vol% trifluoroethanol
41 | d1atga_ |
| not modelled | 10.6 | 13 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
42 | c3cvgC_ |
| not modelled | 10.5 | 14 | PDB header:metal binding protein Chain: C: PDB Molecule:putative metal binding protein; PDBTitle: crystal structure of a periplasmic putative metal binding protein
43 | c1d0rA_ |
| not modelled | 6.9 | 27 | PDB header:hormone/growth factor Chain: A: PDB Molecule:glucagon-like peptide-1-(7-36)-amide; PDBTitle: solution structure of glucagon-like peptide-1-(7-36)-amide2 in trifluoroethanol/water
44 | c2h5yC_ |
| not modelled | 6.4 | 12 | PDB header:metal transport Chain: C: PDB Molecule:molybdate-binding periplasmic protein; PDBTitle: crystallographic structure of the molybdate-binding protein of2 xanthomonas citri at 1.7 ang resolution bound to molybdate

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
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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