Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0CF83
DateThu Jan 5 11:31:41 GMT 2012
Unique Job ID2d3986ad7e85e9a7

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1bcoa2
Top template information
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
Confidence and coverage
Confidence: 99.7% Coverage: 57%
164 residues ( 57% of your sequence) have been modelled with 99.7% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
277 residues ( 96%) 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  MKYVFIEKHQAEFSIKAMCRVLRVARSGWYTWCQRRTRISTRQQFRQHCDSVVLAAFTRS
Secondary structure 












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Disorder  ??
































??????


















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   .........70.........80.........90.........100.........110.........120
Sequence  KQRYGAPRLTDELRAQGYPFNVKTVAASLRRQGLRAKASRKFSPVSYRAHGLPVSENLLE
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??




?









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   .........130.........140.........150.........160.........170.........180
Sequence  QDFYASGPNQKWAGDITYLRTDEGWLYLAVVIDLWSRAVIGWSMSPRMTAQLACDALQMA
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   .........190.........200.........210.........220.........230.........240
Sequence  LWRRKRPRNVIVHTDRGGQYCSADYQAQLKRHNLRGSMSAKGCCYDNACVESFFHSLKVE
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   .........250.........260.........270.........280........
Sequence  CIHGEHFISREIMRATVFNYIECDYNRWRRHSWCGGLSPEQFENKNLA
Secondary structure 

















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????
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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 1bco chain A domain 2

3D model

Region: 124 - 288
Aligned: 164
Modelled: 165
Confidence: 99.7%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2

PDB 3f9k chain V

3D model

Region: 126 - 288
Aligned: 151
Modelled: 163
Confidence: 99.7%
Identity: 17%
PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd

Phyre2

PDB 1c0m chain A domain 2

3D model

Region: 125 - 281
Aligned: 151
Modelled: 157
Confidence: 99.6%
Identity: 22%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1c0m chain A

3D model

Region: 125 - 281
Aligned: 151
Modelled: 157
Confidence: 99.6%
Identity: 22%
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase

Phyre2

PDB 1asu chain A

3D model

Region: 119 - 279
Aligned: 155
Modelled: 161
Confidence: 99.6%
Identity: 20%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1bco chain A

3D model

Region: 124 - 288
Aligned: 163
Modelled: 165
Confidence: 99.5%
Identity: 15%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2

PDB 1exq chain A

3D model

Region: 126 - 288
Aligned: 143
Modelled: 163
Confidence: 99.5%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3nf9 chain A

3D model

Region: 131 - 287
Aligned: 145
Modelled: 157
Confidence: 99.5%
Identity: 20%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design

Phyre2

PDB 3hos chain A

3D model

Region: 2 - 262
Aligned: 249
Modelled: 261
Confidence: 99.4%
Identity: 14%
PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg

Phyre2

PDB 1ex4 chain A

3D model

Region: 126 - 281
Aligned: 140
Modelled: 156
Confidence: 99.4%
Identity: 23%
PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain

Phyre2

PDB 3kks chain B

3D model

Region: 130 - 286
Aligned: 144
Modelled: 157
Confidence: 99.4%
Identity: 17%
PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii

Phyre2

PDB 1cxq chain A

3D model

Region: 125 - 267
Aligned: 135
Modelled: 143
Confidence: 99.3%
Identity: 23%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1k6y chain B

3D model

Region: 121 - 281
Aligned: 140
Modelled: 161
Confidence: 99.3%
Identity: 22%
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase

Phyre2

PDB 1c6v chain A

3D model

Region: 128 - 281
Aligned: 131
Modelled: 154
Confidence: 99.2%
Identity: 21%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1hyv chain A

3D model

Region: 132 - 288
Aligned: 133
Modelled: 157
Confidence: 99.2%
Identity: 23%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3hpg chain C

3D model

Region: 128 - 281
Aligned: 140
Modelled: 154
Confidence: 99.2%
Identity: 18%
PDB header:transferase
Chain: C: PDB Molecule:integrase;
PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces

Phyre2

PDB 3l2t chain B

3D model

Region: 123 - 281
Aligned: 151
Modelled: 158
Confidence: 99.0%
Identity: 16%
PDB header:recombination/dna
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir)

Phyre2

PDB 3dlr chain A

3D model

Region: 126 - 281
Aligned: 138
Modelled: 156
Confidence: 98.5%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase

Phyre2

PDB 6pax chain A

3D model

Region: 2 - 95
Aligned: 94
Modelled: 94
Confidence: 98.4%
Identity: 14%
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

Phyre2

PDB 1u78 chain A

3D model

Region: 2 - 93
Aligned: 87
Modelled: 92
Confidence: 98.4%
Identity: 15%
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

Phyre2
1

d1bcoa2
2

c3f9kV_
3

d1c0ma2
4

c1c0mA_
5

d1asua_
6

c1bcoA_
7

d1exqa_
8

c3nf9A_
9

c3hosA_
10

c1ex4A_
11

c3kksB_
12

d1cxqa_
13

c1k6yB_
14

d1c6va_
15

d1hyva_
16

c3hpgC_
17

c3l2tB_
18

c3dlrA_
19

c6paxA_
20

c1u78A_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1bcoa2



99.7 15 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
2c3f9kV_



99.7 17 PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
3d1c0ma2



99.6 22 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
4c1c0mA_



99.6 22 PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase
5d1asua_



99.6 20 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
6c1bcoA_



99.5 15 PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
7d1exqa_



99.5 18 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
8c3nf9A_



99.5 20 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design
9c3hosA_



99.4 14 PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
10c1ex4A_



99.4 23 PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
11c3kksB_



99.4 17 PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii
12d1cxqa_



99.3 23 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
13c1k6yB_



99.3 22 PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
14d1c6va_



99.2 21 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
15d1hyva_



99.2 23 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
16c3hpgC_



99.2 18 PDB header:transferase
Chain: C: PDB Molecule:integrase;
PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces
17c3l2tB_



99.0 16 PDB header:recombination/dna
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir)
18c3dlrA_



98.5 17 PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase
19c6paxA_



98.4 14 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
20c1u78A_



98.4 15 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
21d1pdnc_



not modelled 98.2 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
22c2k27A_



not modelled 97.7 10 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
23c2f7tA_



not modelled 97.5 16 PDB header:dna binding protein
Chain: A: PDB Molecule:mos1 transposase;
PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase
24c3f2kB_



not modelled 97.2 11 PDB header:transferase
Chain: B: PDB Molecule:histone-lysine n-methyltransferase setmar;
PDBTitle: structure of the transposase domain of human histone-lysine2 n-methyltransferase setmar
25c1hlvA_



not modelled 96.9 17 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
26d2jn6a1



not modelled 96.5 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
27c2elhA_



not modelled 96.3 24 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
28c3hefB_



not modelled 95.8 9 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
29c1umqA_



not modelled 95.7 11 PDB header:dna-binding protein
Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein;
PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
30d1umqa_



not modelled 95.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
31d1k78a1



not modelled 95.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
32d1ntca_



not modelled 94.9 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
33d6paxa1



not modelled 94.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
34d1etxa_



not modelled 94.5 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
35d1fipa_



not modelled 94.4 3 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
36c3e7lD_



not modelled 93.8 15 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
37d1hlva1



not modelled 93.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
38d1g2ha_



not modelled 93.7 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
39d1etob_



not modelled 93.3 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
40d2coba1



not modelled 93.1 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
41c3kjxD_



not modelled 92.2 9 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi
42c3h5tA_



not modelled 92.1 13 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
43c2rn7A_



not modelled 91.9 6 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
44d2bjca1



not modelled 91.9 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
45d1utxa_



not modelled 91.0 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
46c3bs3A_



not modelled 90.7 14 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
47c1z4hA_



not modelled 90.5 9 PDB header:protein binding, dna binding protein
Chain: A: PDB Molecule:tor inhibition protein;
PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase
48c1bdhA_



not modelled 90.3 14 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
49d2icta1



not modelled 90.2 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
50d1adra_



not modelled 90.1 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
51d2ao9a1



not modelled 89.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
52d1rzsa_



not modelled 89.7 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
53d1biaa1



not modelled 89.7 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
54c3cecA_



not modelled 89.7 11 PDB header:transcription
Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system;
PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution
55d1bw6a_



not modelled 89.5 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
56d1jt6a1



not modelled 89.3 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
57c3o60A_



not modelled 89.2 36 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin0861 protein;
PDBTitle: the crystal structure of lin0861 from listeria innocua to 2.8a
58c3omtA_



not modelled 89.2 11 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.
59c1zvvA_



not modelled 89.0 13 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
60d1y9qa1



not modelled 88.8 8 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Probable transcriptional regulator VC1968, N-terminal domain
61c3f1bA_



not modelled 88.8 18 PDB header:transcription regulator
Chain: A: PDB Molecule:tetr-like transcriptional regulator;
PDBTitle: the crystal structure of a tetr-like transcriptional regulator from2 rhodococcus sp. rha1.
62d2hsga1



not modelled 88.6 13 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
63d1t56a1



not modelled 88.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
64d1mkma1



not modelled 88.5 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
65d1vi0a1



not modelled 88.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
66d2fq4a1



not modelled 88.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
67c2lcvA_



not modelled 88.5 14 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional repressor cytr;
PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation
68d1lcda_



not modelled 88.4 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
69c1vi0B_



not modelled 88.4 14 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator
70d1jhfa1



not modelled 88.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
71d1efaa1



not modelled 88.3 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
72d1j5ya1



not modelled 88.3 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
73c2xcjB_



not modelled 88.2 16 PDB header:viral protein
Chain: B: PDB Molecule:c protein;
PDBTitle: crystal structure of p2 c, the immunity repressor of2 temperate e. coli phage p2
74c2l8nA_



not modelled 88.1 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional repressor cytr;
PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna
75c3gpvA_



not modelled 88.1 5 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
76c2cg4B_



not modelled 88.1 6 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
77d2fbqa1



not modelled 88.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
78c2guhA_



not modelled 88.0 14 PDB header:transcription
Chain: A: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: crystal structure of the putative tetr-family transcriptional2 regulator from rhodococcus sp. rha1
79c3kkcB_



not modelled 88.0 18 PDB header:transcription regulator
Chain: B: PDB Molecule:tetr family transcriptional regulator;
PDBTitle: the crystal structure of tetr transcriptional regulator from2 streptococcus agalactiae 2603v
80c2p6tH_



not modelled 87.9 6 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
81d1r8da_



not modelled 87.9 5 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
82c3clcC_



not modelled 87.9 9 PDB header:transcription regulator/dna
Chain: C: PDB Molecule:regulatory protein;
PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator
83c2ppxA_



not modelled 87.9 11 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
84d2ppxa1



not modelled 87.9 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
85c3i4pA_



not modelled 87.8 6 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
86c3ppbB_



not modelled 87.7 18 PDB header:transcription regulator
Chain: B: PDB Molecule:putative tetr family transcription regulator;
PDBTitle: crystal structure of a putative tetr family transcription regulator2 (shew_3104) from shewanella sp. pv-4 at 2.10 a resolution
87c2kpjA_



not modelled 87.7 12 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
88c3b7hA_



not modelled 87.6 12 PDB header:structural protein
Chain: A: PDB Molecule:prophage lp1 protein 11;
PDBTitle: crystal structure of the prophage lp1 protein 11
89c2ia0A_



not modelled 87.5 9 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)
90d3c07a1



not modelled 87.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
91c3b81A_



not modelled 87.4 9 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, acrr family;
PDBTitle: crystal structure of predicted dna-binding transcriptional regulator2 of tetr/acrr family (np_350189.1) from clostridium acetobutylicum at3 2.10 a resolution
92c2nx4A_



not modelled 87.4 0 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.
93c2dg7A_



not modelled 87.4 4 PDB header:gene regulation
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator sco03372 from streptomyces coelicolor a3(2)
94c2l0kA_



not modelled 87.4 9 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
95c2e7xA_



not modelled 87.3 15 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
96c2w48D_



not modelled 87.3 14 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
97d2g3ba1



not modelled 87.2 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
98d1pb6a1



not modelled 87.2 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
99c3op9A_



not modelled 87.2 8 PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua
100d1xsva_



not modelled 87.1 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
101c2of7A_



not modelled 87.1 9 PDB header:transcription
Chain: A: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: structural genomics, the crystal structure of a tetr-family2 transcriptional regulator from streptomyces coelicolor a3
102c2ebyA_



not modelled 87.1 18 PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli
103d1lmb3_



not modelled 87.1 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
104c2vbzA_



not modelled 87.0 9 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
105d2np5a1



not modelled 87.0 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
106c2eh3A_



not modelled 87.0 9 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of aq_1058, a transcriptional regulator (terr/acrr2 family) from aquifex aeolicus vf5
107d1ui5a1



not modelled 87.0 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
108c3bcgA_



not modelled 86.9 18 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator acrr;
PDBTitle: conformational changes of the acrr regulator reveal a2 mechanism of induction
109c2oerA_



not modelled 86.8 14 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional regulator;
PDBTitle: probable transcriptional regulator from pseudomonas2 aeruginosa
110d2vkva1



not modelled 86.8 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
111c3eusB_



not modelled 86.8 14 PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding protein;
PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
112c3on4D_



not modelled 86.7 14 PDB header:transcription
Chain: D: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of tetr transcriptional regulator from legionella2 pneumophila
113d2b5aa1



not modelled 86.7 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
114c3cjdB_



not modelled 86.6 23 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, tetr family;
PDBTitle: crystal structure of putative tetr transcriptional regulator2 (yp_510936.1) from jannaschia sp. ccs1 at 1.79 a resolution
115c3lwjA_



not modelled 86.6 18 PDB header:transcription regulator
Chain: A: PDB Molecule:putative tetr-family transcriptional regulator;
PDBTitle: crystal structure of putative tetr-family transcriptional regulator2 (yp_752756.1) from syntrophomonas wolfei str. goettingen at 2.07 a3 resolution
116d2cg4a1



not modelled 86.6 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
117c1jumB_



not modelled 86.6 5 PDB header:transcription
Chain: B: PDB Molecule:hypothetical transcriptional regulator in qaca
PDBTitle: crystal structure of the multidrug binding transcriptional2 repressor qacr bound to the natural drug berberine
118c2f07A_



not modelled 86.6 14 PDB header:transcription
Chain: A: PDB Molecule:yvdt;
PDBTitle: crystal structure of yvdt from bacillus subtilis
119c2cfxD_



not modelled 86.6 13 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
120c3dcfB_



not modelled 86.6 9 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator of the tetr/acrr
PDBTitle: crystal structure of transcriptional regulator of the2 tetr/acrr family (yp_290855.1) from thermobifida fusca yx-3 er1 at 2.50 a resolution

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
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Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0