Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP33358
DateThu Jan 5 11:51:59 GMT 2012
Unique Job ID058ee72f82c60bf2

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3gpvA_
Top template information
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
Confidence and coverage
Confidence: 99.8% Coverage: 45%
110 residues ( 45% of your sequence) have been modelled with 99.8% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
238 residues ( 98%) 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  MALYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNG
Secondary structure 


























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Disorder  ?????























????
?

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?
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   .........70.........80.........90.........100.........110.........120
Sequence  VQVSKVKMLLSNENVDVQNGWRDQQETLLTYLQSGNLHSLRTWIKERGQDYPAQTLTTHL
Secondary structure 








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Disorder 









?
?????










































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   .........130.........140.........150.........160.........170.........180
Sequence  FIPLRRRLQCQQPTLQALLAILDGVLINYIAICLASARKKQGKDALVVGWNIQDTTRLWL
Secondary structure 














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Disorder 








??
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?????
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   .........190.........200.........210.........220.........230.........240
Sequence  EGWIASQQGWRIDVLAHSLNQLRPELFEGRTLLVWCGENRTSAQQQQLTSWQEQGHDIFP
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Disorder 

















?
??

??











??















????
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   ...
Sequence  LGI
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 3gpv chain A

3D model

Region: 2 - 111
Aligned: 110
Modelled: 109
Confidence: 99.8%
Identity: 19%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis

Phyre2

PDB 1r8d chain A

3D model

Region: 1 - 111
Aligned: 108
Modelled: 111
Confidence: 99.8%
Identity: 25%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2

PDB 2vz4 chain A

3D model

Region: 3 - 98
Aligned: 96
Modelled: 96
Confidence: 99.8%
Identity: 23%
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

Phyre2

PDB 3hh0 chain C

3D model

Region: 4 - 111
Aligned: 108
Modelled: 108
Confidence: 99.8%
Identity: 18%
PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus

Phyre2

PDB 3gp4 chain B

3D model

Region: 4 - 111
Aligned: 108
Modelled: 108
Confidence: 99.8%
Identity: 15%
PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes

Phyre2

PDB 3qao chain A

3D model

Region: 3 - 96
Aligned: 94
Modelled: 92
Confidence: 99.8%
Identity: 19%
PDB header:transcription regulator
Chain: A: PDB Molecule:merr-like transcriptional regulator;
PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e

Phyre2

PDB 2zhh chain A

3D model

Region: 2 - 112
Aligned: 108
Modelled: 111
Confidence: 99.8%
Identity: 19%
PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr

Phyre2

PDB 3d6z chain A

3D model

Region: 3 - 110
Aligned: 105
Modelled: 108
Confidence: 99.8%
Identity: 22%
PDB header:transcription regulator/dna
Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator;
PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine

Phyre2

PDB 1q06 chain A

3D model

Region: 4 - 120
Aligned: 117
Modelled: 117
Confidence: 99.8%
Identity: 14%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2

PDB 1r8e chain A domain 1

3D model

Region: 2 - 95
Aligned: 94
Modelled: 94
Confidence: 99.7%
Identity: 19%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2

PDB 2jml chain A

3D model

Region: 3 - 76
Aligned: 74
Modelled: 74
Confidence: 99.7%
Identity: 28%
PDB header:transcription
Chain: A: PDB Molecule:dna binding domain/transcriptional regulator;
PDBTitle: solution structure of the n-terminal domain of cara repressor

Phyre2

PDB 3ezx chain A

3D model

Region: 82 - 237
Aligned: 156
Modelled: 156
Confidence: 99.6%
Identity: 13%
PDB header:transferase
Chain: A: PDB Molecule:monomethylamine corrinoid protein 1;
PDBTitle: structure of methanosarcina barkeri monomethylamine2 corrinoid protein

Phyre2

PDB 2i2x chain D

3D model

Region: 86 - 238
Aligned: 153
Modelled: 153
Confidence: 99.4%
Identity: 9%
PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri

Phyre2

PDB 2dg6 chain A

3D model

Region: 4 - 84
Aligned: 72
Modelled: 80
Confidence: 99.4%
Identity: 18%
PDB header:gene regulation
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator sco55502 from streptomyces coelicolor a3(2)

Phyre2

PDB 1bmt chain B

3D model

Region: 84 - 238
Aligned: 155
Modelled: 155
Confidence: 99.4%
Identity: 10%
PDB header:methyltransferase
Chain: B: PDB Molecule:methionine synthase;
PDBTitle: how a protein binds b12: a 3.o angstrom x-ray structure of2 the b12-binding domains of methionine synthase

Phyre2

PDB 1k98 chain A

3D model

Region: 84 - 238
Aligned: 155
Modelled: 155
Confidence: 99.0%
Identity: 10%
PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment

Phyre2

PDB 2ev2 chain B

3D model

Region: 4 - 126
Aligned: 121
Modelled: 123
Confidence: 98.5%
Identity: 15%
PDB header:lyase
Chain: B: PDB Molecule:hypothetical protein rv1264/mt1302;
PDBTitle: structure of rv1264n, the regulatory domain of the mycobacterial2 adenylyl cylcase rv1264, at ph 8.5

Phyre2

PDB 1y80 chain A

3D model

Region: 161 - 237
Aligned: 77
Modelled: 77
Confidence: 97.6%
Identity: 10%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted cobalamin binding protein;
PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica

Phyre2

PDB 3bul chain A domain 2

3D model

Region: 159 - 238
Aligned: 80
Modelled: 80
Confidence: 97.4%
Identity: 10%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1q08 chain A

3D model

Region: 46 - 111
Aligned: 66
Modelled: 66
Confidence: 97.2%
Identity: 15%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2
1

c3gpvA_
2

d1r8da_
3

c2vz4A_
4

c3hh0C_
5

c3gp4B_
6

c3qaoA_
7

c2zhhA_
8

c3d6zA_
9

d1q06a_
10

d1r8ea1
11

c2jmlA_
12

c3ezxA_
13

c2i2xD_
14

c2dg6A_
15

c1bmtB_
16

c1k98A_
17

c2ev2B_
18

c1y80A_
19

d3bula2
20

d1q08a_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3gpvA_



99.8 19 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
2d1r8da_



99.8 25 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
3c2vz4A_



99.8 23 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
4c3hh0C_



99.8 18 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus
5c3gp4B_



99.8 15 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes
6c3qaoA_



99.8 19 PDB header:transcription regulator
Chain: A: PDB Molecule:merr-like transcriptional regulator;
PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e
7c2zhhA_



99.8 19 PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr
8c3d6zA_



99.8 22 PDB header:transcription regulator/dna
Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator;
PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine
9d1q06a_



99.8 14 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
10d1r8ea1



99.7 19 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
11c2jmlA_



99.7 28 PDB header:transcription
Chain: A: PDB Molecule:dna binding domain/transcriptional regulator;
PDBTitle: solution structure of the n-terminal domain of cara repressor
12c3ezxA_



99.6 13 PDB header:transferase
Chain: A: PDB Molecule:monomethylamine corrinoid protein 1;
PDBTitle: structure of methanosarcina barkeri monomethylamine2 corrinoid protein
13c2i2xD_



99.4 9 PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri
14c2dg6A_



99.4 18 PDB header:gene regulation
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator sco55502 from streptomyces coelicolor a3(2)
15c1bmtB_



99.4 10 PDB header:methyltransferase
Chain: B: PDB Molecule:methionine synthase;
PDBTitle: how a protein binds b12: a 3.o angstrom x-ray structure of2 the b12-binding domains of methionine synthase
16c1k98A_



99.0 10 PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment
17c2ev2B_



98.5 15 PDB header:lyase
Chain: B: PDB Molecule:hypothetical protein rv1264/mt1302;
PDBTitle: structure of rv1264n, the regulatory domain of the mycobacterial2 adenylyl cylcase rv1264, at ph 8.5
18c1y80A_



97.6 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted cobalamin binding protein;
PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica
19d3bula2



97.4 10 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
20d1q08a_



97.2 15 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
21d1ccwa_



not modelled 96.9 13 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
22c3ezfA_



not modelled 96.6 11 PDB header:biosynthetic protein
Chain: A: PDB Molecule:para;
PDBTitle: partition protein
23c1u78A_



not modelled 96.5 6 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
24c2yxbA_



not modelled 96.4 10 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
25d1xrsb1



not modelled 96.2 13 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
26c1z4hA_



not modelled 95.6 12 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
27d7reqa2



not modelled 95.4 9 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
28c1xrsB_



not modelled 95.3 14 PDB header:isomerase
Chain: B: PDB Molecule:d-lysine 5,6-aminomutase beta subunit;
PDBTitle: crystal structure of lysine 5,6-aminomutase in complex with plp,2 cobalamin, and 5'-deoxyadenosine
29d1fmfa_



not modelled 95.2 12 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
30c1hlvA_



not modelled 95.0 24 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
31d2jn6a1



not modelled 94.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
32c3op9A_



not modelled 93.1 11 PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua
33c2kfsA_



not modelled 92.4 15 PDB header:dna-binding protein
Chain: A: PDB Molecule:conserved hypothetical regulatory protein;
PDBTitle: nmr structure of rv2175c
34d1pdnc_



not modelled 91.2 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
35c3fymA_



not modelled 90.6 12 PDB header:dna binding protein
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: the 1a structure of ymfm, a putative dna-binding membrane2 protein from staphylococcus aureus
36d3bula1



not modelled 90.6 8 Fold:Methionine synthase domain-like
Superfamily:Methionine synthase domain
Family:Methionine synthase domain
37c2rn7A_



not modelled 90.4 29 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
38d1j9ia_



not modelled 89.5 19 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:Terminase gpNU1 subunit domain
39d2b5aa1



not modelled 89.4 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
40d1utxa_



not modelled 88.4 13 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
41c2wusR_



not modelled 87.2 27 PDB header:structural protein
Chain: R: PDB Molecule:putative uncharacterized protein;
PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz
42c6paxA_



not modelled 87.0 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
43d1etxa_



not modelled 86.8 35 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
44d1fipa_



not modelled 86.6 36 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
45c2ppxA_



not modelled 86.1 32 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
46d2ppxa1



not modelled 86.1 32 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
47d2bjca1



not modelled 86.1 22 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
48c3e7lD_



not modelled 85.8 14 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
49c3fmyA_



not modelled 85.6 9 PDB header:dna binding protein
Chain: A: PDB Molecule:hth-type transcriptional regulator mqsa
PDBTitle: structure of the c-terminal domain of the e. coli protein2 mqsa (ygit/b3021)
50c3bd1B_



not modelled 83.4 17 PDB header:transcription
Chain: B: PDB Molecule:cro protein;
PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1
51c2kpjA_



not modelled 83.2 21 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
52c3iwfA_



not modelled 83.1 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator rpir family;
PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
53c3clcC_



not modelled 82.0 18 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
54d1adra_



not modelled 81.6 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
55d1lcda_



not modelled 81.5 22 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
56c3mklB_



not modelled 81.0 15 PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
57c1bdhA_



not modelled 80.3 17 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
58c1zvvA_



not modelled 80.3 20 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
59d1x57a1



not modelled 79.9 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:EDF1-like
60c3gn5B_



not modelled 79.8 11 PDB header:dna binding protein
Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021);
PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
61c3omtA_



not modelled 79.8 23 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.
62c3f52A_



not modelled 79.8 27 PDB header:transcription activator
Chain: A: PDB Molecule:clp gene regulator (clgr);
PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum
63c3ivpD_



not modelled 79.3 14 PDB header:dna binding protein
Chain: D: PDB Molecule:putative transposon-related dna-binding protein;
PDBTitle: the structure of a possible transposon-related dna-binding protein2 from clostridium difficile 630.
64c3bs3A_



not modelled 79.2 18 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
65c3b7hA_



not modelled 79.2 36 PDB header:structural protein
Chain: A: PDB Molecule:prophage lp1 protein 11;
PDBTitle: crystal structure of the prophage lp1 protein 11
66c1umqA_



not modelled 79.0 15 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
67d1umqa_



not modelled 79.0 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
68c3kxaD_



not modelled 78.8 17 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae
69d1r69a_



not modelled 78.5 9 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
70d1qpza1



not modelled 78.0 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
71d1sq8a_



not modelled 77.8 9 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
72d1b0na2



not modelled 77.7 23 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
73c2o8xA_



not modelled 77.6 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
74c3t76A_



not modelled 77.6 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator vanug;
PDBTitle: crystal structure of transcriptional regulator vanug, form ii
75c1y9qA_



not modelled 77.6 18 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, hth_3 family;
PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae
76d2ofya1



not modelled 77.4 27 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
77d2r1jl1



not modelled 77.1 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
78d2croa_



not modelled 76.8 13 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
79c3h5tA_



not modelled 76.6 18 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
80c3k69A_



not modelled 76.6 13 PDB header:transcription
Chain: A: PDB Molecule:putative transcription regulator;
PDBTitle: crystal structure of a putative transcriptional regulator (lp_0360)2 from lactobacillus plantarum at 1.95 a resolution
81c3mlfC_



not modelled 76.3 18 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: putative transcriptional regulator from staphylococcus aureus.
82d1rp3a2



not modelled 76.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
83d1y7ya1



not modelled 76.0 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
84c3dnvB_



not modelled 75.6 23 PDB header:transcription/dna
Chain: B: PDB Molecule:hth-type transcriptional regulator hipb;
PDBTitle: mdt protein
85c1zljE_



not modelled 75.0 17 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
86c1b0nA_



not modelled 75.0 23 PDB header:transcription regulator
Chain: A: PDB Molecule:protein (sinr protein);
PDBTitle: sinr protein/sini protein complex
87c2ef8A_



not modelled 74.5 9 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcription factor;
PDBTitle: crystal structure of c.ecot38is
88c2bnoA_



not modelled 74.0 27 PDB header:oxidoreductase
Chain: A: PDB Molecule:epoxidase;
PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
89c2l8nA_



not modelled 74.0 31 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
90c3mzyA_



not modelled 73.8 22 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
91d1g2ha_



not modelled 73.7 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
92c2xcjB_



not modelled 73.6 18 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
93c1x3uA_



not modelled 73.3 23 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
94d1uxca_



not modelled 73.2 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
95d2hsga1



not modelled 72.9 24 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
96d1bw6a_



not modelled 72.6 35 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
97c2k9sA_



not modelled 72.5 22 PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac
98d1y9qa1



not modelled 72.5 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Probable transcriptional regulator VC1968, N-terminal domain
99c2jvlA_



not modelled 72.1 18 PDB header:transcription
Chain: A: PDB Molecule:trmbf1;
PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
100c3hugA_



not modelled 72.0 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
101c3kjxD_



not modelled 71.9 17 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
102c2ebyA_



not modelled 71.8 23 PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli
103c3f6wE_



not modelled 71.8 14 PDB header:dna binding protein
Chain: E: PDB Molecule:xre-family like protein;
PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000
104c2fjrB_



not modelled 71.7 19 PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186
105d1llib_



not modelled 71.1 9 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
106c3cuoB_



not modelled 70.8 21 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
107d1yioa1



not modelled 70.5 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)
108d1efaa1



not modelled 70.4 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
109d1fsea_



not modelled 70.0 23 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)
110c3trbA_



not modelled 69.9 14 PDB header:dna binding protein
Chain: A: PDB Molecule:virulence-associated protein i;
PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii
111d1or7a1



not modelled 69.5 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
112d1uxda_



not modelled 68.9 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
113c2krfB_



not modelled 68.7 13 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
114d2icta1



not modelled 68.6 23 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
115d1j5ya1



not modelled 68.6 5 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
116c2lcvA_



not modelled 68.4 26 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
117d1rioa_



not modelled 67.9 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
118d1jt6a1



not modelled 67.8 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
119c2elhA_



not modelled 67.8 27 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
120d1a04a1



not modelled 67.8 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)

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