Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP13445
DateThu Jan 5 11:33:34 GMT 2012
Unique Job IDf4e7fa6e4304a16b

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2a6eF_
Top template information
PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
Confidence and coverage
Confidence:100.0% Coverage: 82%
269 residues ( 82% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MSQNTLKVHDLNEDAEFDENGVEVFDEKALVEQEPSDNDLAEEELLSQGATQRVLDATQL
Secondary structure 
SS confidence 
Disorder  ???????
??
???????
??
?????????????????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  YLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLI
Secondary structure 
SS confidence 
Disorder 
???
???
??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  EEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  TARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILAD
Secondary structure 
SS confidence 
Disorder 
??
?
???????
?
????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  EKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRE
Secondary structure 
SS confidence 
Disorder 
??
?
Disorder confidence 
 
   .........310.........320.........330
Sequence  RVRQIQVEGLRRLREILQTQGLNIEALFRE
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 2a6e chain F

3D model

Region: 54 - 327
Aligned: 269
Modelled: 269
Confidence: 100.0%
Identity: 46%
PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme

Phyre2

PDB 3iyd chain F

3D model

Region: 58 - 323
Aligned: 266
Modelled: 266
Confidence: 100.0%
Identity: 40%
PDB header:transcription/dna
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex

Phyre2

PDB 1l9u chain H

3D model

Region: 55 - 327
Aligned: 266
Modelled: 266
Confidence: 100.0%
Identity: 47%
PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution

Phyre2

PDB 1ku2 chain A

3D model

Region: 56 - 222
Aligned: 167
Modelled: 167
Confidence: 100.0%
Identity: 57%
PDB header:transcription
Chain: A: PDB Molecule:sigma factor siga;
PDBTitle: crystal structure of thermus aquaticus rna polymerase sigma2 subunit fragment containing regions 1.2 to 3.1

Phyre2

PDB 1ku2 chain A domain 2

3D model

Region: 55 - 164
Aligned: 110
Modelled: 110
Confidence: 100.0%
Identity: 66%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 1smy chain F domain 3

3D model

Region: 54 - 164
Aligned: 111
Modelled: 111
Confidence: 100.0%
Identity: 66%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 1rp3 chain G

3D model

Region: 86 - 319
Aligned: 216
Modelled: 220
Confidence: 100.0%
Identity: 24%
PDB header:transcription
Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia);
PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm

Phyre2

PDB 1sig chain A

3D model

Region: 58 - 161
Aligned: 104
Modelled: 104
Confidence: 100.0%
Identity: 50%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 1or7 chain A

3D model

Region: 75 - 318
Aligned: 173
Modelled: 179
Confidence: 99.9%
Identity: 18%
PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma-e factor;
PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea

Phyre2

PDB 2q1z chain A

3D model

Region: 72 - 317
Aligned: 174
Modelled: 179
Confidence: 99.9%
Identity: 18%
PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr

Phyre2

PDB 1rp3 chain A domain 3

3D model

Region: 87 - 163
Aligned: 77
Modelled: 77
Confidence: 99.8%
Identity: 27%
Fold: Sigma2 domain of RNA polymerase sigma factors
Superfamily: Sigma2 domain of RNA polymerase sigma factors
Family: Sigma2 domain of RNA polymerase sigma factors

Phyre2

PDB 3mzy chain A

3D model

Region: 117 - 321
Aligned: 119
Modelled: 125
Confidence: 99.8%
Identity: 23%
PDB header:rna binding protein
Chain: A: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a

Phyre2

PDB 1smy chain F domain 2

3D model

Region: 224 - 327
Aligned: 99
Modelled: 104
Confidence: 99.7%
Identity: 29%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 3t72 chain O

3D model

Region: 248 - 323
Aligned: 76
Modelled: 76
Confidence: 99.6%
Identity: 34%
PDB header:transcription/dna
Chain: O: PDB Molecule:pho box dna (strand 1);
PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex

Phyre2

PDB 1ku7 chain A

3D model

Region: 257 - 327
Aligned: 71
Modelled: 71
Confidence: 99.6%
Identity: 35%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1ku3 chain A

3D model

Region: 259 - 316
Aligned: 58
Modelled: 58
Confidence: 99.5%
Identity: 41%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 3hug chain A

3D model

Region: 241 - 324
Aligned: 80
Modelled: 84
Confidence: 99.4%
Identity: 23%
PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl

Phyre2

PDB 2p7v chain B domain 1

3D model

Region: 262 - 323
Aligned: 62
Modelled: 62
Confidence: 99.4%
Identity: 40%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1tty chain A

3D model

Region: 258 - 322
Aligned: 65
Modelled: 65
Confidence: 99.4%
Identity: 42%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1rp3 chain A domain 2

3D model

Region: 245 - 318
Aligned: 70
Modelled: 74
Confidence: 99.3%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2
1
c2a6eF_
2
c3iydF_
3
c1l9uH_
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c1ku2A_
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d1ku2a2
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d1smyf3
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c1rp3G_
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d1siga_
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c1or7A_
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c2q1zA_
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d1rp3a3
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c3mzyA_
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d1smyf2
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c3t72o_
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d1ku7a_
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d1ku3a_
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c3hugA_
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d2p7vb1
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d1ttya_
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d1rp3a2
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2a6eF_
100.0 46 PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
2c3iydF_
100.0 40 PDB header:transcription/dna
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex
3c1l9uH_
100.0 47 PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution
4c1ku2A_
100.0 57 PDB header:transcription
Chain: A: PDB Molecule:sigma factor siga;
PDBTitle: crystal structure of thermus aquaticus rna polymerase sigma2 subunit fragment containing regions 1.2 to 3.1
5d1ku2a2
100.0 66 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
6d1smyf3
100.0 66 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
7c1rp3G_
100.0 24 PDB header:transcription
Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia);
PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm
8d1siga_
100.0 50 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
9c1or7A_
99.9 18 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
10c2q1zA_
99.9 18 PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
11d1rp3a3
99.8 27 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
12c3mzyA_
99.8 23 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
13d1smyf2
99.7 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
14c3t72o_
99.6 34 PDB header:transcription/dna
Chain: O: PDB Molecule:pho box dna (strand 1);
PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex
15d1ku7a_
99.6 35 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
16d1ku3a_
99.5 41 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
17c3hugA_
99.4 23 PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
18d2p7vb1
99.4 40 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
19d1ttya_
99.4 42 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
20d1rp3a2
99.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
21d1or7a2
not modelled 99.3 18 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
22d1or7b2
not modelled 99.3 19 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
23d1or7a1
not modelled 99.1 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
24c2o7gA_
not modelled 99.1 20 PDB header:transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-c factor;
PDBTitle: crystal structure of the pribnow box recognition region of sigc from2 mycobacterium tuberculosis
25d1ku2a1
not modelled 99.0 40 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
26d1xsva_
not modelled 99.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
27d1s7oa_
not modelled 98.9 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
28c2o8xA_
not modelled 98.9 16 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
29c1l0oC_
not modelled 98.8 22 PDB header:protein binding
Chain: C: PDB Molecule:sigma factor;
PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf
30d1l0oc_
not modelled 98.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
31d1h3la_
not modelled 98.5 14 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
32d1rp3a1
not modelled 98.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
33d1yioa1
not modelled 98.2 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)
34c3qp5C_
not modelled 98.0 10 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
35c3n0rA_
not modelled 98.0 10 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: structure of the phyr stress response regulator at 1.25 angstrom2 resolution
36c2q0oA_
not modelled 97.9 13 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
37c1x3uA_
not modelled 97.9 13 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
38c3sztB_
not modelled 97.9 23 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
39c1h0mD_
not modelled 97.8 23 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
40c1zljE_
not modelled 97.8 26 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
41d1a04a1
not modelled 97.8 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)
42c2krfB_
not modelled 97.6 11 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
43c2rnjA_
not modelled 97.6 15 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
44d1fsea_
not modelled 97.6 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
45d1l3la1
not modelled 97.5 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)
46d1p4wa_
not modelled 97.5 19 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)
47c3cloC_
not modelled 97.4 14 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
48c3c3wB_
not modelled 97.4 24 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
49c3klnC_
not modelled 97.2 11 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
50c1zn2A_
not modelled 97.0 13 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
51c2w48D_
not modelled 97.0 17 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
52c2jpcA_
not modelled 96.9 20 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
53c1rnlA_
not modelled 96.7 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
54c1u78A_
not modelled 96.1 21 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
55d2d1ha1
not modelled 95.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
56d1jhfa1
not modelled 95.2 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
57c2bnoA_
not modelled 94.8 27 PDB header:oxidoreductase
Chain: A: PDB Molecule:epoxidase;
PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
58c2w7nA_
not modelled 94.7 21 PDB header:transcription/dna
Chain: A: PDB Molecule:trfb transcriptional repressor protein;
PDBTitle: crystal structure of kora bound to operator dna: insight2 into repressor cooperation in rp4 gene regulation
59c2o38A_
not modelled 94.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: putative xre family transcriptional regulator
60d2o38a1
not modelled 94.1 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
61d2cfxa1
not modelled 94.0 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
62d1pdnc_
not modelled 93.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
63c6paxA_
not modelled 93.8 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
64c2x4hA_
not modelled 93.8 11 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
65d1stza1
not modelled 93.7 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
66d1trra_
not modelled 93.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
67d2ofya1
not modelled 93.6 13 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
68d2cg4a1
not modelled 93.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
69c3r0aB_
not modelled 93.3 9 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
70c3fymA_
not modelled 93.2 20 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
71c2elhA_
not modelled 93.1 17 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
72c3k2zA_
not modelled 93.0 15 PDB header:hydrolase
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: crystal structure of a lexa protein from thermotoga maritima
73c3op9A_
not modelled 92.8 14 PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua
74c2kpjA_
not modelled 92.8 9 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
75c2l4aA_
not modelled 92.7 12 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
76c2p6tH_
not modelled 92.6 11 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
77d1k78a1
not modelled 92.6 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
78c2vbzA_
not modelled 92.6 21 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
79c2cg4B_
not modelled 92.5 14 PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
80d1jhga_
not modelled 92.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
81d2b5aa1
not modelled 92.4 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
82c2fjrB_
not modelled 92.4 14 PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186
83d2a6ca1
not modelled 92.3 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
84d1biaa1
not modelled 92.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
85c2cfxD_
not modelled 92.3 16 PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
86d2cyya1
not modelled 92.3 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
87d2b0la1
not modelled 92.3 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CodY HTH domain
88d1vz0a1
not modelled 92.3 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
89c3f6wE_
not modelled 92.3 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
90c2wteB_
not modelled 92.3 6 PDB header:antiviral protein
Chain: B: PDB Molecule:csa3;
PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution.
91d1nr3a_
not modelled 92.2 19 Fold:DNA-binding protein Tfx
Superfamily:DNA-binding protein Tfx
Family:DNA-binding protein Tfx
92c2r0qF_
not modelled 92.2 22 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
93d2croa_
not modelled 92.1 20 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
94c2dbbA_
not modelled 92.0 13 PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
95d1i1ga1
not modelled 92.0 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
96c3hyiA_
not modelled 91.9 21 PDB header:transcription regulator
Chain: A: PDB Molecule:protein duf199/whia;
PDBTitle: crystal structure of full-length duf199/whia from thermatoga maritima
97c1b0nA_
not modelled 91.8 13 PDB header:transcription regulator
Chain: A: PDB Molecule:protein (sinr protein);
PDBTitle: sinr protein/sini protein complex
98d1adra_
not modelled 91.8 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
99c2e7xA_
not modelled 91.8 14 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
100d1y7ya1
not modelled 91.8 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
101c2it0A_
not modelled 91.7 15 PDB header:transcription/dna
Chain: A: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of a two-domain ider-dna complex crystal2 form ii
102c1y9qA_
not modelled 91.5 17 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
103c3frwF_
not modelled 91.4 12 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
104c2ia0A_
not modelled 91.3 11 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)
105c3kxaD_
not modelled 91.3 11 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae
106c3nqoB_
not modelled 91.1 15 PDB header:transcription
Chain: B: PDB Molecule:marr-family transcriptional regulator;
PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
107c3clcC_
not modelled 91.1 22 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
108d1ft9a1
not modelled 91.0 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
109d1i5za1
not modelled 91.0 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
110c2e1cA_
not modelled 90.9 14 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
111c2wusR_
not modelled 90.9 13 PDB header:structural protein
Chain: R: PDB Molecule:putative uncharacterized protein;
PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz
112c3f52A_
not modelled 90.8 11 PDB header:transcription activator
Chain: A: PDB Molecule:clp gene regulator (clgr);
PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum
113d2oz6a1
not modelled 90.7 37 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
114c1i1gA_
not modelled 90.7 11 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
115d2ao9a1
not modelled 90.7 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
116c3mlfC_
not modelled 90.7 9 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: putative transcriptional regulator from staphylococcus aureus.
117c3korD_
not modelled 90.7 10 PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
118c3fmyA_
not modelled 90.7 11 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)
119c1r22B_
not modelled 90.7 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
120d6paxa1
not modelled 90.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired 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
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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