Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP07026
DateThu Jan 5 11:00:07 GMT 2012
Unique Job IDce222fa25bfdf73e

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1h0mD_
Top template information
PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna
Confidence and coverage
Confidence:100.0% Coverage: 92%
222 residues ( 92% 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 

   1........10.........20.........30.........40.........50.........60
Sequence  MQDKDFFSWRRTMLLRFQRMETAEEVYHEIELQAQQLEYDYYSLCVRHPVPFTRPKVAFY
Secondary structure 




















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Disorder  ???????







































?????







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   .........70.........80.........90.........100.........110.........120
Sequence  TNYPEAWVSYYQAKNFLAIDPVLNPENFSQGHLMWNDDLFSEAQPLWEAARAHGLRRGVT
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   .........130.........140.........150.........160.........170.........180
Sequence  QYLMLPNRALGFLSFSRCSAREIPILSDELQLKMQLLVRESLMALMRLNDEIVMTPEMNF
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?
?????





















??????????????
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   .........190.........200.........210.........220.........230.........240
Sequence  SKREKEILRWTAEGKTSAEIAMILSISENTVNFHQKNMQKKINAPNKTQVACYAAATGLI
Secondary structure 















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????
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Sequence 
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

RankAligned region

PDB 1h0m chain D

3D model

Region: 9 - 240
Aligned: 222
Modelled: 232
Confidence: 100.0%
Identity: 19%
PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna

Phyre2

PDB 2q0o chain A

3D model

Region: 2 - 240
Aligned: 229
Modelled: 239
Confidence: 100.0%
Identity: 22%
PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing

Phyre2

PDB 3szt chain B

3D model

Region: 11 - 240
Aligned: 222
Modelled: 230
Confidence: 100.0%
Identity: 31%
PDB header:transcription
Chain: B: PDB Molecule:quorum-sensing control repressor;
PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone

Phyre2

PDB 3qp5 chain C

3D model

Region: 12 - 239
Aligned: 216
Modelled: 228
Confidence: 100.0%
Identity: 26%
PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)

Phyre2

PDB 2avx chain A

3D model

Region: 1 - 171
Aligned: 171
Modelled: 171
Confidence: 100.0%
Identity: 99%
PDB header:transcription
Chain: A: PDB Molecule:regulatory protein sdia;
PDBTitle: solution structure of e coli sdia1-171

Phyre2

PDB 1l3l chain A domain 2

3D model

Region: 9 - 175
Aligned: 161
Modelled: 167
Confidence: 99.8%
Identity: 16%
Fold: Profilin-like
Superfamily: Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
Family: Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

Phyre2

PDB 2uv0 chain G

3D model

Region: 12 - 168
Aligned: 157
Modelled: 157
Confidence: 99.8%
Identity: 20%
PDB header:transcription
Chain: G: PDB Molecule:transcriptional activator protein lasr;
PDBTitle: structure of the p. aeruginosa lasr ligand-binding domain2 bound to its autoinducer

Phyre2

PDB 3qp1 chain A

3D model

Region: 12 - 169
Aligned: 153
Modelled: 158
Confidence: 99.8%
Identity: 20%
PDB header:transcription
Chain: A: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir ligand-binding domain bound to the native2 ligand c6-hsl

Phyre2

PDB 3clo chain C

3D model

Region: 177 - 240
Aligned: 64
Modelled: 64
Confidence: 99.8%
Identity: 41%
PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution

Phyre2

PDB 2krf chain B

3D model

Region: 172 - 240
Aligned: 69
Modelled: 69
Confidence: 99.7%
Identity: 23%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a

Phyre2

PDB 1l3l chain A domain 1

3D model

Region: 176 - 240
Aligned: 65
Modelled: 65
Confidence: 99.7%
Identity: 28%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: GerE-like (LuxR/UhpA family of transcriptional regulators)

Phyre2

PDB 1zlj chain E

3D model

Region: 176 - 240
Aligned: 65
Modelled: 65
Confidence: 99.7%
Identity: 25%
PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain

Phyre2

PDB 1p4w chain A

3D model

Region: 172 - 240
Aligned: 69
Modelled: 69
Confidence: 99.7%
Identity: 26%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: GerE-like (LuxR/UhpA family of transcriptional regulators)

Phyre2

PDB 1fse chain A

3D model

Region: 177 - 240
Aligned: 64
Modelled: 64
Confidence: 99.7%
Identity: 31%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: GerE-like (LuxR/UhpA family of transcriptional regulators)

Phyre2

PDB 1a04 chain A domain 1

3D model

Region: 174 - 239
Aligned: 66
Modelled: 66
Confidence: 99.7%
Identity: 29%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: GerE-like (LuxR/UhpA family of transcriptional regulators)

Phyre2

PDB 2rnj chain A

3D model

Region: 180 - 240
Aligned: 61
Modelled: 61
Confidence: 99.7%
Identity: 36%
PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain

Phyre2

PDB 3c3w chain B

3D model

Region: 174 - 237
Aligned: 64
Modelled: 64
Confidence: 99.7%
Identity: 25%
PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr

Phyre2

PDB 1x3u chain A

3D model

Region: 180 - 240
Aligned: 61
Modelled: 61
Confidence: 99.7%
Identity: 31%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein fixj;
PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot

Phyre2

PDB 3kln chain C

3D model

Region: 155 - 236
Aligned: 82
Modelled: 82
Confidence: 99.7%
Identity: 33%
PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst

Phyre2

PDB 1rnl chain A

3D model

Region: 178 - 239
Aligned: 62
Modelled: 62
Confidence: 99.6%
Identity: 31%
PDB header:signal transduction protein
Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl;
PDBTitle: the nitrate/nitrite response regulator protein narl from narl

Phyre2
1

c1h0mD_
2

c2q0oA_
3

c3sztB_
4

c3qp5C_
5

c2avxA_
6

d1l3la2
7

c2uv0G_
8

c3qp1A_
9

c3cloC_
10

c2krfB_
11

d1l3la1
12

c1zljE_
13

d1p4wa_
14

d1fsea_
15

d1a04a1
16

c2rnjA_
17

c3c3wB_
18

c1x3uA_
19

c3klnC_
20

c1rnlA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1h0mD_



100.0 19 PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna
2c2q0oA_



100.0 22 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
3c3sztB_



100.0 31 PDB header:transcription
Chain: B: PDB Molecule:quorum-sensing control repressor;
PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone
4c3qp5C_



100.0 26 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
5c2avxA_



100.0 99 PDB header:transcription
Chain: A: PDB Molecule:regulatory protein sdia;
PDBTitle: solution structure of e coli sdia1-171
6d1l3la2



99.8 16 Fold:Profilin-like
Superfamily:Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
Family:Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
7c2uv0G_



99.8 20 PDB header:transcription
Chain: G: PDB Molecule:transcriptional activator protein lasr;
PDBTitle: structure of the p. aeruginosa lasr ligand-binding domain2 bound to its autoinducer
8c3qp1A_



99.8 20 PDB header:transcription
Chain: A: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir ligand-binding domain bound to the native2 ligand c6-hsl
9c3cloC_



99.8 41 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution
10c2krfB_



99.7 23 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
11d1l3la1



99.7 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
12c1zljE_



99.7 25 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
13d1p4wa_



99.7 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
14d1fsea_



99.7 31 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
15d1a04a1



99.7 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
16c2rnjA_



99.7 36 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
17c3c3wB_



99.7 25 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
18c1x3uA_



99.7 31 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein fixj;
PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
19c3klnC_



99.7 33 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
20c1rnlA_



99.6 31 PDB header:signal transduction protein
Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl;
PDBTitle: the nitrate/nitrite response regulator protein narl from narl
21c2jpcA_



not modelled 99.6 34 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
22d1yioa1



not modelled 99.6 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
23c1zn2A_



not modelled 99.6 27 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
24d1ttya_



not modelled 98.4 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
25c1kgsA_



not modelled 98.3 25 PDB header:dna binding protein
Chain: A: PDB Molecule:dna binding response regulator d;
PDBTitle: crystal structure at 1.50 a of an ompr/phob homolog from thermotoga2 maritima
26d2p7vb1



not modelled 98.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
27d1smyf2



not modelled 98.2 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
28d1rp3a2



not modelled 98.2 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
29d1xsva_



not modelled 98.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
30d1ku7a_



not modelled 98.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
31c2o8xA_



not modelled 98.2 14 PDB header:transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-c factor;
PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc
32d1or7a1



not modelled 98.1 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
33c3hugA_



not modelled 98.1 23 PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
34d1ku3a_



not modelled 98.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
35d1s7oa_



not modelled 98.0 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
36c3mzyA_



not modelled 98.0 37 PDB header:rna binding protein
Chain: A: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a
37c3q9sA_



not modelled 98.0 25 PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding response regulator;
PDBTitle: crystal structure of rra(1-215) from deinococcus radiodurans
38c1rp3G_



not modelled 98.0 23 PDB header:transcription
Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia);
PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm
39c1or7A_



not modelled 97.9 19 PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma-e factor;
PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea
40c2q1zA_



not modelled 97.7 9 PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
41c3t72o_



not modelled 97.5 16 PDB header:transcription/dna
Chain: O: PDB Molecule:pho box dna (strand 1);
PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex
42c2oqrA_



not modelled 97.5 19 PDB header:transcription,signaling protein
Chain: A: PDB Molecule:sensory transduction protein regx3;
PDBTitle: the structure of the response regulator regx3 from mycobacterium2 tuberculosis
43c1l9uH_



not modelled 97.4 16 PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution
44c2a6eF_



not modelled 97.3 14 PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
45d1jhfa1



not modelled 97.2 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
46c2hqrA_



not modelled 97.1 13 PDB header:signaling protein
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism
47d2cg4a1



not modelled 97.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
48c1ys7B_



not modelled 96.9 25 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulatory protein prra;
PDBTitle: crystal structure of the response regulator protein prra comlexed with2 mg2+
49d1stza1



not modelled 96.8 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
50c2gwrA_



not modelled 96.8 16 PDB header:signaling protein
Chain: A: PDB Molecule:dna-binding response regulator mtra;
PDBTitle: crystal structure of the response regulator protein mtra from2 mycobacterium tuberculosis
51c3p7nB_



not modelled 96.6 28 PDB header:dna binding protein
Chain: B: PDB Molecule:sensor histidine kinase;
PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis
52c3k2zA_



not modelled 96.5 23 PDB header:hydrolase
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: crystal structure of a lexa protein from thermotoga maritima
53c1u78A_



not modelled 96.5 14 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
54c2wteB_



not modelled 96.4 27 PDB header:antiviral protein
Chain: B: PDB Molecule:csa3;
PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution.
55c3r0jA_



not modelled 96.4 22 PDB header:dna binding protein
Chain: A: PDB Molecule:possible two component system response transcriptional
PDBTitle: structure of phop from mycobacterium tuberculosis
56d1biaa1



not modelled 96.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
57c2l4aA_



not modelled 96.3 9 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
58d2cyya1



not modelled 96.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
59d1i1ga1



not modelled 96.3 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
60d2d1ha1



not modelled 96.3 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
61d2cfxa1



not modelled 96.3 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
62c1p2fA_



not modelled 96.1 28 PDB header:transcription
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure analysis of response regulator drrb, a2 thermotoga maritima ompr/phob homolog
63c2cg4B_



not modelled 96.1 19 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
64c2e1cA_



not modelled 96.1 19 PDB header:transcription/dna
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519;
PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex
65d1j5ya1



not modelled 96.1 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
66c3iydF_



not modelled 96.1 16 PDB header:transcription/dna
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex
67c2dbbA_



not modelled 96.0 16 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
68c2vbzA_



not modelled 96.0 19 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
69c2p6tH_



not modelled 95.9 21 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
70c2e7xA_



not modelled 95.9 21 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
71c1i1gA_



not modelled 95.7 33 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
72c3r0aB_



not modelled 95.7 19 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
73c2x4hA_



not modelled 95.6 29 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
74c2ewnA_



not modelled 95.5 15 PDB header:ligase, transcription
Chain: A: PDB Molecule:bira bifunctional protein;
PDBTitle: ecoli biotin repressor with co-repressor analog
75c2cfxD_



not modelled 95.3 9 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
76d2oola1



not modelled 95.3 12 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
77c2ia0A_



not modelled 95.2 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)
78c3cuoB_



not modelled 95.2 20 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
79c6paxA_



not modelled 95.0 19 PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeobox protein pax-6;
PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions
80c2fa5B_



not modelled 95.0 7 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
81c1b9nA_



not modelled 94.9 15 PDB header:transcription
Chain: A: PDB Molecule:protein (mode);
PDBTitle: regulator from escherichia coli
82d1r1ua_



not modelled 94.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
83d1sfxa_



not modelled 94.9 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
84d1r71a_



not modelled 94.9 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
85d1pdnc_



not modelled 94.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
86c2r0qF_



not modelled 94.8 21 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
87c1r71B_



not modelled 94.7 28 PDB header:transcription/dna
Chain: B: PDB Molecule:transcriptional repressor protein korb;
PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna
88c3tgnA_



not modelled 94.7 29 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
89c3i4pA_



not modelled 94.7 19 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
90c2vn2B_



not modelled 94.7 17 PDB header:replication
Chain: B: PDB Molecule:chromosome replication initiation protein;
PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426
91d1r1ta_



not modelled 94.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
92d1lnwa_



not modelled 94.6 3 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
93d1okra_



not modelled 94.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
94d1k78a1



not modelled 94.5 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
95c2it0A_



not modelled 94.5 30 PDB header:transcription/dna
Chain: A: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of a two-domain ider-dna complex crystal2 form ii
96c1r22B_



not modelled 94.4 15 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
97c2gm4B_



not modelled 94.4 19 PDB header:recombination, dna
Chain: B: PDB Molecule:transposon gamma-delta resolvase;
PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna
98d1gxqa_



not modelled 94.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:PhoB-like
99c2oqgA_



not modelled 94.4 22 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
100c3frwF_



not modelled 94.4 19 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
101d2o9ca1



not modelled 94.3 8 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
102c2zxjB_



not modelled 94.3 18 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein walr;
PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus
103d1vz0a1



not modelled 94.2 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
104d6paxa1



not modelled 94.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
105c2hwvA_



not modelled 94.2 23 PDB header:transcription
Chain: A: PDB Molecule:dna-binding response regulator vicr;
PDBTitle: crystal structure of an essential response regulator dna binding2 domain, vicrc in enterococcus faecalis, a member of the yycf3 subfamily.
106c3korD_



not modelled 94.0 22 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
107c2x48B_



not modelled 94.0 28 PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
108c3trcA_



not modelled 93.9 8 PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of the gaf domain from a phosphoenolpyruvate-protein2 phosphotransferase (ptsp) from coxiella burnetii
109c2v79B_



not modelled 93.9 19 PDB header:dna-binding protein
Chain: B: PDB Molecule:dna replication protein dnad;
PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis
110c3f6oB_



not modelled 93.9 17 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
111d2p4wa1



not modelled 93.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
112c3nqoB_



not modelled 93.8 23 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
113c2elhA_



not modelled 93.8 21 PDB header:dna binding protein
Chain: A: PDB Molecule:cg11849-pa;
PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa
114c1f5tA_



not modelled 93.8 33 PDB header:transcription/dna
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence
115d3broa1



not modelled 93.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
116d2a61a1



not modelled 93.7 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
117c2nyxB_



not modelled 93.6 11 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
118d2g9wa1



not modelled 93.6 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
119c2nnnB_



not modelled 93.5 8 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulator;
PDBTitle: crystal structure of probable transcriptional regulator from2 pseudomonas aeruginosa
120d1kgsa1



not modelled 93.4 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:PhoB-like

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