Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionQ47274
DateThu Jan 5 12:36:44 GMT 2012
Unique Job ID7e6a50281b4ae4ae

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3hugA_
Top template information
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
Confidence and coverage
Confidence: 99.1% Coverage: 54%
69 residues ( 54% of your sequence) have been modelled with 99.1% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

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



















SS confidence 



























































Disorder  ???














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   .........70.........80.........90.........100.........110.........120
Sequence  KKNNSDLHDLLVDYYVVGMTFMSLAGKHCCSDGYIGKRLQKAEGIIEGMLMALDIRLEMD
Secondary structure 








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?




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   .......
Sequence  IVVNNSN
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 3hug chain A

3D model

Region: 48 - 116
Aligned: 69
Modelled: 69
Confidence: 99.1%
Identity: 16%
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

Phyre2

PDB 1or7 chain A domain 1

3D model

Region: 47 - 110
Aligned: 61
Modelled: 64
Confidence: 99.0%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1rp3 chain A domain 2

3D model

Region: 48 - 111
Aligned: 64
Modelled: 64
Confidence: 99.0%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 2o8x chain A

3D model

Region: 48 - 107
Aligned: 57
Modelled: 60
Confidence: 98.9%
Identity: 21%
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

Phyre2

PDB 1s7o chain A

3D model

Region: 53 - 124
Aligned: 72
Modelled: 72
Confidence: 98.9%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: YlxM/p13-like

Phyre2

PDB 1xsv chain A

3D model

Region: 51 - 115
Aligned: 65
Modelled: 65
Confidence: 98.8%
Identity: 9%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: YlxM/p13-like

Phyre2

PDB 1rp3 chain G

3D model

Region: 48 - 111
Aligned: 64
Modelled: 64
Confidence: 98.8%
Identity: 11%
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

Phyre2

PDB 1or7 chain A

3D model

Region: 39 - 110
Aligned: 72
Modelled: 71
Confidence: 98.7%
Identity: 14%
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

Phyre2

PDB 2q1z chain A

3D model

Region: 47 - 110
Aligned: 64
Modelled: 64
Confidence: 98.6%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr

Phyre2

PDB 3mzy chain A

3D model

Region: 47 - 111
Aligned: 65
Modelled: 65
Confidence: 98.6%
Identity: 14%
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

Phyre2

PDB 1ku7 chain A

3D model

Region: 58 - 118
Aligned: 61
Modelled: 61
Confidence: 98.4%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1tty chain A

3D model

Region: 54 - 106
Aligned: 53
Modelled: 53
Confidence: 98.4%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1smy chain F domain 2

3D model

Region: 31 - 118
Aligned: 87
Modelled: 88
Confidence: 98.4%
Identity: 9%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1ku3 chain A

3D model

Region: 60 - 107
Aligned: 48
Modelled: 48
Confidence: 98.3%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 2p7v chain B domain 1

3D model

Region: 60 - 106
Aligned: 47
Modelled: 47
Confidence: 98.1%
Identity: 13%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 3t72 chain O

3D model

Region: 48 - 107
Aligned: 60
Modelled: 60
Confidence: 97.8%
Identity: 10%
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

Phyre2

PDB 1yio chain A domain 1

3D model

Region: 54 - 106
Aligned: 52
Modelled: 53
Confidence: 97.6%
Identity: 8%
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 1x3u chain A

3D model

Region: 54 - 106
Aligned: 52
Modelled: 53
Confidence: 97.6%
Identity: 17%
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 1l9u chain H

3D model

Region: 48 - 118
Aligned: 71
Modelled: 71
Confidence: 97.5%
Identity: 10%
PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution

Phyre2

PDB 1a04 chain A domain 1

3D model

Region: 60 - 106
Aligned: 46
Modelled: 47
Confidence: 97.2%
Identity: 9%
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
1

c3hugA_
2

d1or7a1
3

d1rp3a2
4

c2o8xA_
5

d1s7oa_
6

d1xsva_
7

c1rp3G_
8

c1or7A_
9

c2q1zA_
10

c3mzyA_
11

d1ku7a_
12

d1ttya_
13

d1smyf2
14

d1ku3a_
15

d2p7vb1
16

c3t72o_
17

d1yioa1
18

c1x3uA_
19

c1l9uH_
20

d1a04a1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3hugA_



99.1 16 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
2d1or7a1



99.0 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
3d1rp3a2



99.0 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
4c2o8xA_



98.9 21 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
5d1s7oa_



98.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
6d1xsva_



98.8 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
7c1rp3G_



98.8 11 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
8c1or7A_



98.7 14 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
9c2q1zA_



98.6 13 PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
10c3mzyA_



98.6 14 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
11d1ku7a_



98.4 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
12d1ttya_



98.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
13d1smyf2



98.4 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
14d1ku3a_



98.3 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
15d2p7vb1



98.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
16c3t72o_



97.8 10 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
17d1yioa1



97.6 8 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)
18c1x3uA_



97.6 17 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
19c1l9uH_



97.5 10 PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution
20d1a04a1



97.2 9 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)
21c2w48D_



not modelled 97.2 18 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
22c1zljE_



not modelled 97.2 13 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
23c2a6eF_



not modelled 97.1 9 PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
24c2krfB_



not modelled 97.0 16 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
25d1l3la1



not modelled 97.0 16 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)
26c2rnjA_



not modelled 96.9 7 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
27c3qp5C_



not modelled 96.9 9 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
28c2q0oA_



not modelled 96.8 19 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
29d1fsea_



not modelled 96.8 12 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)
30c3sztB_



not modelled 96.8 9 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
31c1u78A_



not modelled 96.7 13 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
32c1h0mD_



not modelled 96.6 16 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
33d1pdnc_



not modelled 96.2 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
34c6paxA_



not modelled 96.2 15 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
35c3c3wB_



not modelled 96.2 11 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
36c3klnC_



not modelled 96.0 16 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
37c3cloC_



not modelled 95.9 12 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
38c2jpcA_



not modelled 95.7 11 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
39c3iydF_



not modelled 95.7 12 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
40d1p4wa_



not modelled 95.6 17 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)
41d1k78a1



not modelled 95.4 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
42c1rnlA_



not modelled 95.3 5 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
43c2r0qF_



not modelled 95.1 5 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
44c3n0rA_



not modelled 95.0 17 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: structure of the phyr stress response regulator at 1.25 angstrom2 resolution
45c1zn2A_



not modelled 94.7 8 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
46d6paxa1



not modelled 94.6 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
47d2jn6a1



not modelled 94.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
48d2cfxa1



not modelled 93.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
49c2dbbA_



not modelled 93.4 20 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
50c3onqB_



not modelled 93.2 12 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:regulator of polyketide synthase expression;
PDBTitle: crystal structure of regulator of polyketide synthase expression2 bad_0249 from bifidobacterium adolescentis
51d2cg4a1



not modelled 93.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
52c2vbzA_



not modelled 92.4 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
53c1hlvA_



not modelled 92.3 6 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:major centromere autoantigen b;
PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna
54d1hlva1



not modelled 92.3 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
55c2ia0A_



not modelled 92.2 15 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)
56c2gm4B_



not modelled 92.2 8 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
57c2cfxD_



not modelled 92.1 13 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
58c3hefB_



not modelled 91.8 10 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
59c2l4aA_



not modelled 91.7 15 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
60c2p6tH_



not modelled 91.7 18 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
61c2cg4B_



not modelled 91.6 18 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
62d1r71a_



not modelled 91.6 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
63c2rn7A_



not modelled 91.4 16 PDB header:unknown function
Chain: A: PDB Molecule:is629 orfa;
PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125
64d1i1ga1



not modelled 91.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
65d1biaa1



not modelled 91.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
66c2k27A_



not modelled 91.1 18 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
67d2cyya1



not modelled 91.0 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
68d1vz0a1



not modelled 90.9 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
69c1r71B_



not modelled 90.4 13 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
70c1r22B_



not modelled 90.3 16 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
71c3i4pA_



not modelled 90.2 21 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
72c2e7xA_



not modelled 90.1 10 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
73c2x48B_



not modelled 90.0 21 PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
74c2elhA_



not modelled 89.8 7 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
75c2e1cA_



not modelled 89.6 7 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
76c3r0aB_



not modelled 89.2 4 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
77c1i1gA_



not modelled 88.6 18 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
78d2d1ha1



not modelled 88.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
79d1jhfa1



not modelled 88.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
80d2fx0a1



not modelled 87.6 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
81d2i10a1



not modelled 86.0 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
82d1j5ya1



not modelled 86.0 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
83d1jt6a1



not modelled 85.3 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
84c3g7rB_



not modelled 85.0 9 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of sco4454, a tetr-family transcriptional2 regulator from streptomyces coelicolor
85d1bw6a_



not modelled 84.9 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
86c1ui6B_



not modelled 84.7 14 PDB header:antibiotic
Chain: B: PDB Molecule:a-factor receptor homolog;
PDBTitle: crystal structure of gamma-butyrolactone receptor (arpa-like protein)
87d1stza1



not modelled 84.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
88d2fbqa1



not modelled 83.6 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
89c1zx4B_



not modelled 83.3 21 PDB header:translation
Chain: B: PDB Molecule:plasmid partition par b protein;
PDBTitle: structure of parb bound to dna
90c2jk3A_



not modelled 83.3 7 PDB header:transcription
Chain: A: PDB Molecule:hemolysin ii regulatory protein;
PDBTitle: crystal structure of the hlyiir mutant protein with2 residues 169-186 substituted by gssgssg linker
91c3dewA_



not modelled 82.9 20 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: the structure of a putative tetr family transcriptional regulator from2 geobacter sulfurreducens pca.
92d2fxaa1



not modelled 82.6 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
93c2dg8D_



not modelled 82.2 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)
94d2g7sa1



not modelled 82.0 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
95d1sfxa_



not modelled 82.0 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
96c3pvpA_



not modelled 81.8 5 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna
97c2gqqB_



not modelled 81.6 13 PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
98d1pb6a1



not modelled 81.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
99d2g3ba1



not modelled 81.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
100c2l0kA_



not modelled 81.1 18 PDB header:transcription
Chain: A: PDB Molecule:stage iii sporulation protein d;
PDBTitle: nmr solution structure of a transcription factor spoiiid in complex2 with dna
101d2gfna1



not modelled 81.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
102c3tgnA_



not modelled 80.9 14 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
103c2g7sA_



not modelled 80.7 5 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: the crystal structure of transcriptional regulator, tetr family, from2 agrobacterium tumefaciens
104d3c07a1



not modelled 80.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
105c3f3xA_



not modelled 80.4 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family, putative;
PDBTitle: crystal structure of the transcriptional regulator bldr2 from sulfolobus solfataricus
106d2esna1



not modelled 80.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LysR-like transcriptional regulators
107c2hytA_



not modelled 80.4 7 PDB header:transcription
Chain: A: PDB Molecule:tetr-family transcriptional regulator;
PDBTitle: crystal structure of a tetr-family transcriptional regulator (eca1819)2 from pectobacterium atrosepticum at 1.64 a resolution
108d1rr7a_



not modelled 80.0 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Middle operon regulator, Mor
109c1rr7A_



not modelled 80.0 13 PDB header:transcription
Chain: A: PDB Molecule:middle operon regulator;
PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu
110d2fq4a1



not modelled 79.9 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
111c3jthA_



not modelled 79.9 11 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
112d1v7ba1



not modelled 79.7 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
113d2vkva1



not modelled 79.6 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
114c2g3bB_



not modelled 79.5 16 PDB header:transcription
Chain: B: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: crystal structure of putative tetr-family transcriptional regulator2 from rhodococcus sp.
115d1r1ua_



not modelled 79.4 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
116d2d6ya1



not modelled 79.3 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
117c3fiwB_



not modelled 79.3 14 PDB header:transcription regulator
Chain: B: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: structure of sco0253, a tetr-family transcriptional regulator from2 streptomyces coelicolor
118d2np5a1



not modelled 79.3 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
119c2nx4A_



not modelled 79.0 9 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:transcriptional regulator, tetr family protein;
PDBTitle: the crystal structure of athe putative tetr-family transcriptional2 regulator rha06780 from rhodococcus sp. rha1.
120c2d6yA_



not modelled 78.9 9 PDB header:gene regulation
Chain: A: PDB Molecule:putative tetr family regulatory protein;
PDBTitle: crystal structure of transcriptional factor sco4008 from streptomyces2 coelicolor a3(2)

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