Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP37007
DateThu Jan 5 11:54:19 GMT 2012
Unique Job IDf577d5c72ac70204

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1bcoA_
Top template information
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
Confidence and coverage
Confidence: 99.9% Coverage: 60%
229 residues ( 60% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
358 residues ( 93%) 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  MESLMPWDARDTMSLRTEFVLFASQDGANIRSLCRRFGISPATGYKWLQRWAQEGAAGLQ
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Disorder  ???????
???













?


























???????
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   .........70.........80.........90.........100.........110.........120
Sequence  DRPRIPHHSPNRSSDDITALLRMAHDRHERWGARKIKRWLEDQGHTMPAFSTVHNLMARH
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Disorder  ??????????????













































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   .........130.........140.........150.........160.........170.........180
Sequence  GLLPGASPGIPATGRFEHDAPNRLWQMDFKGHFPFGGGRCHPLTLLDDHSRFSLCLAHCT
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Disorder 
??????????????












































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   .........190.........200.........210.........220.........230.........240
Sequence  DERRETVQQQLVSVFERYGLPDRMTMDNGSPWGDTTGTWTALELWLMRLGIRVGHSRPYH
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   .........250.........260.........270.........280.........290.........300
Sequence  PQTQGKLERFHRSLKAEVLQGKWFADSGELQRAFDHWRTVYNLERPHEALDMAVPGSRYQ
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   .........310.........320.........330.........340.........350.........360
Sequence  PSARQYSGNTTPPEYDEGVMVRKVDISGKLSVKGVSLSAGKAFRGERVGLKEMQEDGSYE
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   .........370.........380....
Sequence  VWWYSTKVGVIDLKKKSITMGKGC
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 1bco chain A

3D model

Region: 137 - 366
Aligned: 229
Modelled: 229
Confidence: 99.9%
Identity: 17%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2

PDB 1bco chain A domain 2

3D model

Region: 140 - 311
Aligned: 172
Modelled: 172
Confidence: 99.9%
Identity: 13%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2

PDB 3f9k chain V

3D model

Region: 138 - 299
Aligned: 147
Modelled: 162
Confidence: 99.8%
Identity: 18%
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: 136 - 299
Aligned: 155
Modelled: 164
Confidence: 99.8%
Identity: 22%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1c0m chain A

3D model

Region: 136 - 299
Aligned: 157
Modelled: 164
Confidence: 99.8%
Identity: 21%
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: 134 - 294
Aligned: 154
Modelled: 156
Confidence: 99.7%
Identity: 21%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3nf9 chain A

3D model

Region: 140 - 304
Aligned: 149
Modelled: 165
Confidence: 99.7%
Identity: 21%
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 1exq chain A

3D model

Region: 139 - 301
Aligned: 140
Modelled: 163
Confidence: 99.6%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1ex4 chain A

3D model

Region: 139 - 309
Aligned: 152
Modelled: 171
Confidence: 99.6%
Identity: 18%
PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain

Phyre2

PDB 1cxq chain A

3D model

Region: 140 - 283
Aligned: 133
Modelled: 144
Confidence: 99.6%
Identity: 23%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3hos chain A

3D model

Region: 14 - 281
Aligned: 264
Modelled: 268
Confidence: 99.6%
Identity: 15%
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 3kks chain B

3D model

Region: 143 - 305
Aligned: 147
Modelled: 163
Confidence: 99.6%
Identity: 23%
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 3hpg chain C

3D model

Region: 139 - 299
Aligned: 145
Modelled: 161
Confidence: 99.5%
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: 138 - 307
Aligned: 160
Modelled: 170
Confidence: 99.5%
Identity: 20%
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 1hyv chain A

3D model

Region: 141 - 301
Aligned: 133
Modelled: 161
Confidence: 99.5%
Identity: 21%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1c6v chain A

3D model

Region: 139 - 302
Aligned: 138
Modelled: 159
Confidence: 99.5%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1k6y chain B

3D model

Region: 139 - 298
Aligned: 136
Modelled: 160
Confidence: 99.5%
Identity: 20%
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase

Phyre2

PDB 6pax chain A

3D model

Region: 6 - 118
Aligned: 108
Modelled: 113
Confidence: 99.3%
Identity: 18%
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 1pdn chain C

3D model

Region: 6 - 117
Aligned: 107
Modelled: 112
Confidence: 99.3%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 3dlr chain A

3D model

Region: 139 - 299
Aligned: 141
Modelled: 161
Confidence: 99.2%
Identity: 18%
PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase

Phyre2
1

c1bcoA_
2

d1bcoa2
3

c3f9kV_
4

d1c0ma2
5

c1c0mA_
6

d1asua_
7

c3nf9A_
8

d1exqa_
9

c1ex4A_
10

d1cxqa_
11

c3hosA_
12

c3kksB_
13

c3hpgC_
14

c3l2tB_
15

d1hyva_
16

d1c6va_
17

c1k6yB_
18

c6paxA_
19

d1pdnc_
20

c3dlrA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1bcoA_



99.9 17 PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
2d1bcoa2



99.9 13 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
3c3f9kV_



99.8 18 PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
4d1c0ma2



99.8 22 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
5c1c0mA_



99.8 21 PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase
6d1asua_



99.7 21 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
7c3nf9A_



99.7 21 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
8d1exqa_



99.6 18 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
9c1ex4A_



99.6 18 PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
10d1cxqa_



99.6 23 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
11c3hosA_



99.6 15 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
12c3kksB_



99.6 23 PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii
13c3hpgC_



99.5 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
14c3l2tB_



99.5 20 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)
15d1hyva_



99.5 21 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
16d1c6va_



99.5 15 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
17c1k6yB_



99.5 20 PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
18c6paxA_



99.3 18 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
19d1pdnc_



99.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
20c3dlrA_



99.2 18 PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase
21c2k27A_



not modelled 98.9 16 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
22c1u78A_



not modelled 98.9 16 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
23d2jn6a1



not modelled 98.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
24d1k78a1



not modelled 98.0 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
25c1hlvA_



not modelled 98.0 13 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
26d6paxa1



not modelled 97.9 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
27c2rn7A_



not modelled 97.9 17 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
28c2elhA_



not modelled 97.4 19 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
29c2w48D_



not modelled 97.3 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
30d1bcoa1



not modelled 97.2 9 Fold:mu transposase, C-terminal domain
Superfamily:mu transposase, C-terminal domain
Family:mu transposase, C-terminal domain
31d1hlva1



not modelled 97.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
32c3e7lD_



not modelled 97.2 6 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
33d1ntca_



not modelled 97.1 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
34c1umqA_



not modelled 97.0 14 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
35d1umqa_



not modelled 97.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
36c3hefB_



not modelled 97.0 18 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
37d1fipa_



not modelled 96.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
38d1bw6a_



not modelled 96.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
39d1jhga_



not modelled 96.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
40c2f7tA_



not modelled 96.8 17 PDB header:dna binding protein
Chain: A: PDB Molecule:mos1 transposase;
PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase
41d1trra_



not modelled 96.7 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
42d1etxa_



not modelled 96.7 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
43c3sztB_



not modelled 96.4 11 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
44d1etob_



not modelled 96.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
45c3frwF_



not modelled 96.3 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
46c2q0oA_



not modelled 96.3 17 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
47d1r1ua_



not modelled 96.3 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
48c1h0mD_



not modelled 96.2 9 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
49c3korD_



not modelled 96.2 18 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
50c1zljE_



not modelled 96.2 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
51d1g2ha_



not modelled 96.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
52d1r1ta_



not modelled 96.1 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
53d1j5ya1



not modelled 96.1 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
54c1r22B_



not modelled 96.0 17 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
55c3jthA_



not modelled 96.0 14 PDB header:transcription
Chain: A: PDB Molecule:transcription activator hlyu;
PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6
56c3f2kB_



not modelled 96.0 23 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
57d1biaa1



not modelled 95.9 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
58c2oqgA_



not modelled 95.9 22 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
59c2ia0A_



not modelled 95.9 13 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)
60d1a04a1



not modelled 95.9 15 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)
61c2jscB_



not modelled 95.8 9 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050;
PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis
62c1iufA_



not modelled 95.8 15 PDB header:dna binding protein
Chain: A: PDB Molecule:centromere abp1 protein;
PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein
63c2krfB_



not modelled 95.8 14 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
64c2cg4B_



not modelled 95.8 21 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
65d2coba1



not modelled 95.7 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Psq domain
66c2vbzA_



not modelled 95.7 26 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
67d1p4wa_



not modelled 95.7 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)
68c3cuoB_



not modelled 95.6 17 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
69c3c3wB_



not modelled 95.6 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
70c2cfxD_



not modelled 95.6 18 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
71c3qp5C_



not modelled 95.6 14 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
72c1j5yA_



not modelled 95.6 9 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family;
PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution
73c3i4pA_



not modelled 95.6 15 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
74c1x3uA_



not modelled 95.4 26 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
75c1rnlA_



not modelled 95.4 16 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
76c3pqkD_



not modelled 95.4 16 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
77c2p6tH_



not modelled 95.3 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
78c2e7xA_



not modelled 95.3 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
79c2f07A_



not modelled 95.3 19 PDB header:transcription
Chain: A: PDB Molecule:yvdt;
PDBTitle: crystal structure of yvdt from bacillus subtilis
80c2kkoB_



not modelled 95.3 14 PDB header:dna binding protein
Chain: B: PDB Molecule:possible transcriptional regulatory protein
PDBTitle: solution nmr structure of the homodimeric winged helix-turn-2 helix dna-binding domain (fragment 1-100) mb0332 from3 mycobacterium bovis, a possible arsr-family transcriptional4 regulator. northeast structural genomics consortium target5 mbr242e.
81d1q06a_



not modelled 95.3 13 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
82c1or7A_



not modelled 95.2 10 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
83c3f6oB_



not modelled 95.1 17 PDB header:transcription regulator
Chain: B: PDB Molecule:probable transcriptional regulator, arsr family
PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566
84d2d1ha1



not modelled 95.1 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
85d1yioa1



not modelled 95.1 20 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)
86d1fsea_



not modelled 95.1 13 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)
87d1l3la1



not modelled 95.1 10 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)
88c1r71B_



not modelled 95.1 17 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
89c2zhhA_



not modelled 95.0 11 PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr
90d2p4wa1



not modelled 95.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
91c2kpjA_



not modelled 95.0 19 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
92d2ezla_



not modelled 95.0 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
93d1xsva_



not modelled 94.9 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
94d1ulya_



not modelled 94.9 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein PH1932
95c1z4hA_



not modelled 94.9 11 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
96c2vz4A_



not modelled 94.8 17 PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional activator tipa;
PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna
97c1i1gA_



not modelled 94.8 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
98d1r8da_



not modelled 94.8 15 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
99d1vz0a1



not modelled 94.8 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
100c2e1cA_



not modelled 94.8 18 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
101c3mzyA_



not modelled 94.8 15 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
102c2dbbA_



not modelled 94.7 13 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
103c3f6vA_



not modelled 94.7 17 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
104d1i1ga1



not modelled 94.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
105c3by6C_



not modelled 94.7 11 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
106c3klnC_



not modelled 94.6 13 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
107d2cg4a1



not modelled 94.6 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
108c3gpvA_



not modelled 94.6 10 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
109d1r71a_



not modelled 94.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
110c2zkzC_



not modelled 94.6 9 PDB header:transcription
Chain: C: PDB Molecule:transcriptional repressor pagr;
PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis
111c3cloC_



not modelled 94.5 19 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
112d1s7oa_



not modelled 94.5 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
113c3hugA_



not modelled 94.4 13 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
114c3hh0C_



not modelled 94.4 10 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus
115d1stza1



not modelled 94.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
116c2ewnA_



not modelled 94.3 17 PDB header:ligase, transcription
Chain: A: PDB Molecule:bira bifunctional protein;
PDBTitle: ecoli biotin repressor with co-repressor analog
117c2jpcA_



not modelled 94.3 18 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
118d1u2wa1



not modelled 94.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
119c2l4aA_



not modelled 94.2 21 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
120c2rnjA_



not modelled 94.2 12 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain

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