Phyre 2 Results for P0AD37

Phyre Home | Retrieve Phyre Job Id

Email | l.a.kelley@imperial.ac.uk
Description | P0AD37
Date | Thu Jan 5 11:19:54 GMT 2012
Unique Job ID | 774d8878fbf24622

Summary |

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

Model (left) based on template d1tnsa_
Top template information
Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like
Confidence and coverage
Confidence: | 99.8% | Coverage: | 58%
66 residues ( 58% of your sequence) have been modelled with 99.8% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
93 residues ( 82%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | T | P | D | E | L | A | R | L | T | G | Y | S | R | Q | T | I | N | K | W | V | R | K | E | G | W | T | T | S | P | K | P | G | V | Q | G | G | K | A | R | L | V | H | V | N | E | Q | V | R | E | Y | I | R | N | A | E | R | P | E | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? |  |  |  |  |  |  |  | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | .
Sequence |  | Q | G | E | A | P | A | L | S | G | D | A | P | L | E | V | L | L | V | T | L | A | K | E | M | T | P | V | E | Q | K | Q | F | T | S | L | L | L | R | E | G | I | I | G | L | L | Q | R | L | G | I | R | D | S | K
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 |
| d1tnsa_ |

### PDB 1tns chain A

Region: 1 - 66
Aligned: 66
Modelled: 66
Confidence: 99.8%
Identity: 29%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: Excisionase-like

Phyre2
2 |
| d1qpma_ |

### PDB 1qpm chain A

Region: 1 - 58
Aligned: 58
Modelled: 58
Confidence: 99.8%
Identity: 26%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: Excisionase-like

Phyre2
3 |
| d2etha1 |

### PDB 2eth chain A domain 1

Region: 1 - 98
Aligned: 83
Modelled: 83
Confidence: 93.0%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
4 |
| c3k0lA_ |

### PDB 3k0l chain A

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 92.0%
Identity: 16%
PDB header:transcription regulator
Chain: A: PDB Molecule:repressor protein;
PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp

Phyre2
5 |
| d1lj9a_ |

### PDB 1lj9 chain A

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 92.0%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
6 |
| c3nqoB_ |

### PDB 3nqo chain B

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 91.4%
Identity: 24%
PDB header:transcription
Chain: B: PDB Molecule:marr-family transcriptional regulator;
PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution

Phyre2
7 |
| c3nrvC_ |

### PDB 3nrv chain C

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 90.7%
Identity: 14%
PDB header:transcription regulator
Chain: C: PDB Molecule:putative transcriptional regulator (marr/emrr family);
PDBTitle: crystal structure of marr/emrr family transcriptional regulator from2 acinetobacter sp. adp1

Phyre2
8 |
| d1s3ja_ |

### PDB 1s3j chain A

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 90.3%
Identity: 10%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
9 |
| c2nnnB_ |

### PDB 2nnn chain B

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 90.3%
Identity: 25%
PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulator;
PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa

Phyre2
10 |
| d3broa1 |

### PDB 3bro chain A domain 1

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 90.0%
Identity: 8%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
11 |
| c3bjaA_ |

### PDB 3bja chain A

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 89.9%
Identity: 16%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of putative marr-like transcription regulator2 (np_978771.1) from bacillus cereus atcc 10987 at 2.38 a resolution

Phyre2
12 |
| c2qwwB_ |

### PDB 2qww chain B

Region: 1 - 107
Aligned: 89
Modelled: 107
Confidence: 89.8%
Identity: 10%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution

Phyre2
13 |
| d1lnwa_ |

### PDB 1lnw chain A

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 89.3%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
14 |
| c3bj6B_ |

### PDB 3bj6 chain B

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 88.4%
Identity: 18%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579

Phyre2
15 |
| c3bddD_ |

### PDB 3bdd chain D

Region: 1 - 98
Aligned: 76
Modelled: 76
Confidence: 88.4%
Identity: 22%
PDB header:transcription
Chain: D: PDB Molecule:regulatory protein marr;
PDBTitle: crystal structure of a putative multiple antibiotic-resistance2 repressor (ssu05_1136) from streptococcus suis 89/1591 at 2.20 a3 resolution

Phyre2
16 |
| c3bpxB_ |

### PDB 3bpx chain B

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 88.4%
Identity: 20%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of marr

Phyre2
17 |
| c2gxgA_ |

### PDB 2gxg chain A

Region: 1 - 98
Aligned: 83
Modelled: 84
Confidence: 87.8%
Identity: 14%
PDB header:transcription
Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator;
PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7

Phyre2
18 |
| c3cjnA_ |

### PDB 3cjn chain A

Region: 1 - 112
Aligned: 90
Modelled: 98
Confidence: 87.0%
Identity: 14%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi

Phyre2
19 |
| c2nyxB_ |

### PDB 2nyx chain B

Region: 1 - 114
Aligned: 94
Modelled: 100
Confidence: 85.9%
Identity: 15%
PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis

Phyre2
20 |
| c3kp3B_ |

### PDB 3kp3 chain B

Region: 1 - 108
Aligned: 85
Modelled: 85
Confidence: 85.8%
Identity: 13%
PDB header:transcription regulator/antibiotic
Chain: B: PDB Molecule:transcriptional regulator tcar;
PDBTitle: staphylococcus epidermidis in complex with ampicillin

Phyre2
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |
56 |
57 |
58 |
59 |
60 |
61 |
62 |
63 |
64 |
65 |
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
74 |
75 |
76 |
77 |
78 |
79 |
80 |
81 |
82 |
83 |
84 |
85 |
86 |
87 |
88 |
89 |
90 |
91 |
92 |
93 |
94 |
95 |
96 |
97 |
98 |
99 |
100 |
101 |
102 |
103 |
104 |
105 |
106 |
107 |
108 |
109 |
110 |
111 |
112 |
113 |
114 |
115 |
116 |
117 |
118 |
119 |
120 |
121 |
122 |
123 |
124 |
125 |
126 |
127 |
128 |
129 |
130 |
131 |
132 |
133 |
134 |
135 |
136 |
137 |
138 |
139 |
140 |
141 |
142 |
143 |
144 |
145 |
146 |
147 |
148 |
149 |
150 |
151 |
152 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1tnsa_ |
|  | 99.8 | 29 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like
2 | d1qpma_ |
|  | 99.8 | 26 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like
3 | d2etha1 |
|  | 93.0 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
4 | c3k0lA_ |
|  | 92.0 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:repressor protein; PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp
5 | d1lj9a_ |
|  | 92.0 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
6 | c3nqoB_ |
|  | 91.4 | 24 | PDB header:transcription Chain: B: PDB Molecule:marr-family transcriptional regulator; PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
7 | c3nrvC_ |
|  | 90.7 | 14 | PDB header:transcription regulator Chain: C: PDB Molecule:putative transcriptional regulator (marr/emrr family); PDBTitle: crystal structure of marr/emrr family transcriptional regulator from2 acinetobacter sp. adp1
8 | d1s3ja_ |
|  | 90.3 | 10 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
9 | c2nnnB_ |
|  | 90.3 | 25 | PDB header:transcription Chain: B: PDB Molecule:probable transcriptional regulator; PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa
10 | d3broa1 |
|  | 90.0 | 8 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
11 | c3bjaA_ |
|  | 89.9 | 16 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, marr family, putative; PDBTitle: crystal structure of putative marr-like transcription regulator2 (np_978771.1) from bacillus cereus atcc 10987 at 2.38 a resolution
12 | c2qwwB_ |
|  | 89.8 | 10 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution
13 | d1lnwa_ |
|  | 89.3 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
14 | c3bj6B_ |
|  | 88.4 | 18 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of marr family transcription regulator sp03579
15 | c3bddD_ |
|  | 88.4 | 22 | PDB header:transcription Chain: D: PDB Molecule:regulatory protein marr; PDBTitle: crystal structure of a putative multiple antibiotic-resistance2 repressor (ssu05_1136) from streptococcus suis 89/1591 at 2.20 a3 resolution
16 | c3bpxB_ |
|  | 88.4 | 20 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of marr
17 | c2gxgA_ |
|  | 87.8 | 14 | PDB header:transcription Chain: A: PDB Molecule:146aa long hypothetical transcriptional regulator; PDBTitle: crystal structure of emrr homolog from hyperthermophilic archaea2 sulfolobus tokodaii strain7
18 | c3cjnA_ |
|  | 87.0 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of transcriptional regulator, marr family, from2 silicibacter pomeroyi
19 | c2nyxB_ |
|  | 85.9 | 15 | PDB header:transcription Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404; PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
20 | c3kp3B_ |
|  | 85.8 | 13 | PDB header:transcription regulator/antibiotic Chain: B: PDB Molecule:transcriptional regulator tcar; PDBTitle: staphylococcus epidermidis in complex with ampicillin
21 | c3e6mD_ |
| not modelled | 84.7 | 17 | PDB header:transcription regulator Chain: D: PDB Molecule:marr family transcriptional regulator; PDBTitle: the crystal structure of a marr family transcriptional2 regulator from silicibacter pomeroyi dss.
22 | c3g3zA_ |
| not modelled | 84.2 | 14 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, marr family; PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
23 | c2rdpA_ |
| not modelled | 84.0 | 16 | PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator marr; PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
24 | d1ku9a_ |
| not modelled | 82.7 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DNA-binding protein Mj223
25 | d1sd4a_ |
| not modelled | 82.1 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Penicillinase repressor
26 | d2fbia1 |
| not modelled | 80.5 | 18 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
27 | c3deuB_ |
| not modelled | 80.2 | 14 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator slya; PDBTitle: crystal structure of transcription regulatory protein slya2 from salmonella typhimurium in complex with salicylate3 ligands
28 | d2fbha1 |
| not modelled | 79.4 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
29 | d2a61a1 |
| not modelled | 78.1 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
30 | c2fa5B_ |
| not modelled | 78.0 | 12 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator marr/emrr family; PDBTitle: the crystal structure of an unliganded multiple antibiotic-2 resistance repressor (marr) from xanthomonas campestris
31 | d2hr3a1 |
| not modelled | 76.9 | 16 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
32 | d2fbka1 |
| not modelled | 75.9 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
33 | d3deua1 |
| not modelled | 74.7 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
34 | d1sfxa_ |
| not modelled | 74.4 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
35 | d1jgsa_ |
| not modelled | 74.3 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
36 | c3tgnA_ |
| not modelled | 73.7 | 24 | PDB header:transcription Chain: A: PDB Molecule:adc operon repressor adcr; PDBTitle: crystal structure of the zinc-dependent marr family transcriptional2 regulator adcr in the zn(ii)-bound state
37 | c3ecoB_ |
| not modelled | 72.8 | 16 | PDB header:transcription Chain: B: PDB Molecule:mepr; PDBTitle: crystal structure of mepr, a transcription regulator of the2 staphylococcus aureus multidrug efflux pump mepa
38 | d2d1ha1 |
| not modelled | 72.1 | 21 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like
39 | d1okra_ |
| not modelled | 70.4 | 11 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Penicillinase repressor
40 | c2pexA_ |
| not modelled | 67.3 | 23 | PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator ohrr; PDBTitle: structure of reduced c22s ohrr from xanthamonas campestris
41 | d1ub9a_ |
| not modelled | 66.2 | 7 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
42 | d1z91a1 |
| not modelled | 66.1 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
43 | c3s2wB_ |
| not modelled | 64.3 | 12 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: the crystal structure of a marr transcriptional regulator from2 methanosarcina mazei go1
44 | d1j9ia_ |
| not modelled | 64.0 | 25 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Terminase gpNU1 subunit domain
45 | c3ctaA_ |
| not modelled | 60.5 | 26 | PDB header:transferase Chain: A: PDB Molecule:riboflavin kinase; PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
46 | d3ctaa1 |
| not modelled | 58.9 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
47 | c3boqB_ |
| not modelled | 58.7 | 9 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of marr family transcriptional regulator from2 silicibacter pomeroyi
48 | c3r0aB_ |
| not modelled | 58.7 | 11 | PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
49 | c3f6oB_ |
| not modelled | 57.6 | 18 | PDB header:transcription regulator Chain: B: PDB Molecule:probable transcriptional regulator, arsr family PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
50 | c3f3xA_ |
| not modelled | 53.0 | 22 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, marr family, putative; PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
51 | c3fm5D_ |
| not modelled | 52.2 | 20 | PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator; PDBTitle: x-ray crystal structure of transcriptional regulator (marr family)2 from rhodococcus sp. rha1
52 | c2oqgA_ |
| not modelled | 51.6 | 27 | PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
53 | d1r1ta_ |
| not modelled | 49.4 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
54 | d3e5ua1 |
| not modelled | 46.7 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
55 | d1z05a1 |
| not modelled | 45.8 | 20 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain
56 | d2oz6a1 |
| not modelled | 44.9 | 31 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
57 | c1r22B_ |
| not modelled | 44.9 | 19 | PDB header:transcription repressor Chain: B: PDB Molecule:transcriptional repressor smtb; PDBTitle: crystal structure of the cyanobacterial metallothionein2 repressor smtb (c14s/c61s/c121s mutant) in the zn2alpha5-3 form
58 | d1ft9a1 |
| not modelled | 44.4 | 38 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
59 | d1xsva_ |
| not modelled | 44.4 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
60 | c2ppxA_ |
| not modelled | 43.7 | 20 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1735; PDBTitle: crystal structure of a hth xre-family like protein from agrobacterium2 tumefaciens
61 | d2ppxa1 |
| not modelled | 43.7 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like
62 | d2gaua1 |
| not modelled | 43.1 | 19 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
63 | c3f6vA_ |
| not modelled | 42.6 | 25 | PDB header:transcription regulator Chain: A: PDB Molecule:possible transcriptional regulator, arsr family PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
64 | d1hsja1 |
| not modelled | 42.3 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
65 | c3oopA_ |
| not modelled | 41.2 | 18 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2960 protein; PDBTitle: the structure of a protein with unknown function from listeria innocua2 clip11262
66 | d2bgca1 |
| not modelled | 40.4 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
67 | d1r1ua_ |
| not modelled | 40.3 | 7 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators
68 | c3iwfA_ |
| not modelled | 40.2 | 22 | PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
69 | d2cg4a1 |
| not modelled | 40.1 | 39 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
70 | c3omtA_ |
| not modelled | 39.9 | 25 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae.
71 | c3mlfC_ |
| not modelled | 39.5 | 35 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: putative transcriptional regulator from staphylococcus aureus.
72 | d1q06a_ |
| not modelled | 39.4 | 21 | Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators
73 | c2l4aA_ |
| not modelled | 38.3 | 26 | PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp
74 | c3cuoB_ |
| not modelled | 37.1 | 24 | PDB header:transcription regulator Chain: B: PDB Molecule:uncharacterized hth-type transcriptional regulator ygav; PDBTitle: crystal structure of the predicted dna-binding transcriptional2 regulator from e. coli
75 | d2p4wa1 |
| not modelled | 37.1 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PF1790-like
76 | d1p4xa2 |
| not modelled | 36.5 | 9 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
77 | d1biaa1 |
| not modelled | 36.1 | 30 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
78 | d2frha1 |
| not modelled | 35.7 | 17 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
79 | d2coha1 |
| not modelled | 35.1 | 39 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
80 | c2jmlA_ |
| not modelled | 34.8 | 32 | PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor
81 | c2kfsA_ |
| not modelled | 34.5 | 17 | PDB header:dna-binding protein Chain: A: PDB Molecule:conserved hypothetical regulatory protein; PDBTitle: nmr structure of rv2175c
82 | d1p4xa1 |
| not modelled | 33.9 | 13 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators
83 | c3fmyA_ |
| not modelled | 33.8 | 15 | PDB header:dna binding protein Chain: A: PDB Molecule:hth-type transcriptional regulator mqsa PDBTitle: structure of the c-terminal domain of the e. coli protein2 mqsa (ygit/b3021)
84 | d1i5za1 |
| not modelled | 33.4 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like
85 | c2kpjA_ |
| not modelled | 33.4 | 45 | PDB header:transcription regulator Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa; PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a
86 | d2p7vb1 |
| not modelled | 33.4 | 22 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
87 | c3jthA_ |
| not modelled | 33.1 | 16 | PDB header:transcription Chain: A: PDB Molecule:transcription activator hlyu; PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
88 | c2zkzC_ |
| not modelled | 32.3 | 10 | PDB header:transcription Chain: C: PDB Molecule:transcriptional repressor pagr; PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis
89 | c3cdhB_ |
| not modelled | 32.0 | 15 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of the marr family transcriptional regulator spo14532 from silicibacter pomeroyi dss-3
90 | c2cg4B_ |
| not modelled | 31.9 | 39 | PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc
91 | c2e7xA_ |
| not modelled | 31.5 | 26 | PDB header:transcription regulator Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator; PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand
92 | c2zhhA_ |
| not modelled | 31.3 | 26 | PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr
93 | c1i1gA_ |
| not modelled | 31.0 | 26 | PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
94 | d1j5ya1 |
| not modelled | 30.5 | 32 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like
95 | d1i1ga1 |
| not modelled | 30.3 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
96 | c2ia0A_ |
| not modelled | 30.2 | 26 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864; PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864)
97 | c2fjrB_ |
| not modelled | 30.2 | 9 | PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186
98 | c3jw4C_ |
| not modelled | 29.7 | 19 | PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, marr/emrr family; PDBTitle: the structure of a putative marr family transcriptional regulator from2 clostridium acetobutylicum
99 | c2ebyA_ |
| not modelled | 29.4 | 25 | PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli
100 | d1s7oa_ |
| not modelled | 29.4 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like
101 | c2dbbA_ |
| not modelled | 29.4 | 35 | PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061
102 | c3op9A_ |
| not modelled | 29.1 | 15 | PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua
103 | c2qufB_ |
| not modelled | 29.0 | 16 | PDB header:transcription Chain: B: PDB Molecule:transcription factor pf0095; PDBTitle: crystal structure of transcription factor axxa-pf0095 from pyrococcus2 furiosus
104 | c3pqkD_ |
| not modelled | 28.8 | 19 | PDB header:transcription Chain: D: PDB Molecule:biofilm growth-associated repressor; PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
105 | c2vbzA_ |
| not modelled | 28.6 | 35 | PDB header:dna-binding protein Chain: A: PDB Molecule:transcriptional regulatory protein; PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan
106 | c3gp4B_ |
| not modelled | 28.5 | 26 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes
107 | c3bs3A_ |
| not modelled | 28.3 | 40 | PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of a putative dna-binding protein from bacteroides2 fragilis
108 | d1ku3a_ |
| not modelled | 28.2 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain
109 | c3bd1B_ |
| not modelled | 28.0 | 26 | PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1
110 | d2cyya1 |
| not modelled | 27.2 | 30 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
111 | c2p6tH_ |
| not modelled | 27.2 | 17 | PDB header:transcription Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family; PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis
112 | c3f52A_ |
| not modelled | 27.1 | 25 | PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum
113 | d2cfxa1 |
| not modelled | 27.0 | 26 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
114 | c1ft9A_ |
| not modelled | 27.0 | 38 | PDB header:transcription Chain: A: PDB Molecule:carbon monoxide oxidation system transcription PDBTitle: structure of the reduced (feii) co-sensing protein from r.2 rubrum
115 | c3dkwB_ |
| not modelled | 26.8 | 12 | PDB header:transcription regulator Chain: B: PDB Molecule:dnr protein; PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.
116 | d1llib_ |
| not modelled | 26.8 | 20 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
117 | d2croa_ |
| not modelled | 26.7 | 40 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
118 | d1r69a_ |
| not modelled | 26.6 | 30 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors
119 | c2jscB_ |
| not modelled | 26.0 | 21 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050; PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
120 | c2jvlA_ |
| not modelled | 25.9 | 30 | PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei

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