Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP00579
DateThu Jan 5 10:56:46 GMT 2012
Unique Job ID6a3a384d74f72d6f

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3iydF_
Top template information
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
Confidence and coverage
Confidence:100.0% Coverage: 78%
478 residues ( 78% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
610 residues (100%) 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  MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
Secondary structure 
SS confidence 
Disorder  ????
?
???
?
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  DADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA
Secondary structure 
SS confidence 
Disorder  ??????????????????????????????????
????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH
Secondary structure 
SS confidence 
Disorder 
????????????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  VGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR
Secondary structure 
SS confidence 
Disorder  ?????????????????????????????????
?
??
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  SHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK
Secondary structure 
SS confidence 
Disorder  ??
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  NFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKD
Secondary structure 
SS confidence 
Disorder 
????????
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE
Secondary structure 
SS confidence 
Disorder 
??????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP
Secondary structure 
SS confidence 
Disorder 
??
??
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL
Secondary structure 
SS confidence 
Disorder 
??
?
????
??
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  RAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........610...
Sequence  PSRSEVLRSFLDD
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 3iyd chain F

3D model

Region: 114 - 611
Aligned: 478
Modelled: 478
Confidence: 100.0%
Identity: 96%
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 2a6e chain F

3D model

Region: 346 - 612
Aligned: 262
Modelled: 262
Confidence: 100.0%
Identity: 59%
PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme

Phyre2

PDB 1l9u chain H

3D model

Region: 363 - 612
Aligned: 243
Modelled: 243
Confidence: 100.0%
Identity: 56%
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: 349 - 507
Aligned: 159
Modelled: 159
Confidence: 100.0%
Identity: 60%
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 1sig chain A

3D model

Region: 114 - 446
Aligned: 304
Modelled: 304
Confidence: 100.0%
Identity: 86%
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: 373 - 611
Aligned: 216
Modelled: 239
Confidence: 100.0%
Identity: 25%
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 1ku2 chain A domain 2

3D model

Region: 349 - 449
Aligned: 101
Modelled: 101
Confidence: 100.0%
Identity: 60%
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: 349 - 449
Aligned: 101
Modelled: 101
Confidence: 100.0%
Identity: 60%
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 A domain 3

3D model

Region: 373 - 448
Aligned: 76
Modelled: 76
Confidence: 99.8%
Identity: 28%
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 3t72 chain O

3D model

Region: 533 - 613
Aligned: 81
Modelled: 81
Confidence: 99.7%
Identity: 95%
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 1smy chain F domain 2

3D model

Region: 509 - 612
Aligned: 99
Modelled: 104
Confidence: 99.7%
Identity: 56%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1ku7 chain A

3D model

Region: 542 - 612
Aligned: 71
Modelled: 71
Confidence: 99.6%
Identity: 56%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 2p7v chain B domain 1

3D model

Region: 546 - 613
Aligned: 68
Modelled: 68
Confidence: 99.6%
Identity: 100%
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: 540 - 612
Aligned: 73
Modelled: 73
Confidence: 99.5%
Identity: 62%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1or7 chain A

3D model

Region: 359 - 608
Aligned: 171
Modelled: 185
Confidence: 99.4%
Identity: 22%
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 3mzy chain A

3D model

Region: 402 - 610
Aligned: 118
Modelled: 124
Confidence: 99.4%
Identity: 31%
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 1ku3 chain A

3D model

Region: 544 - 602
Aligned: 59
Modelled: 59
Confidence: 99.4%
Identity: 56%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 2q1z chain A

3D model

Region: 356 - 599
Aligned: 170
Modelled: 177
Confidence: 99.3%
Identity: 20%
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 1ku2 chain A domain 1

3D model

Region: 450 - 507
Aligned: 58
Modelled: 58
Confidence: 99.2%
Identity: 59%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma3 domain

Phyre2

PDB 1l0o chain C

3D model

Region: 447 - 502
Aligned: 56
Modelled: 56
Confidence: 98.9%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family: Sigma4 domain

Phyre2

PDB 1cii chain A

3D model

Region: 3 - 445
Aligned: 438
Modelled: 438
Confidence: 97.9%
Identity: 12%
PDB header:transmembrane protein
Chain: A: PDB Molecule:colicin ia;
PDBTitle: colicin ia

Phyre2

PDB 2k6x chain A

3D model

Region: 2 - 55
Aligned: 54
Modelled: 54
Confidence: 97.1%
Identity: 28%
PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: autoregulation of a group 1 bacterial sigma factor involves2 the formation of a region 1.1- induced compacted structure

Phyre2
1
c3iydF_
2
c2a6eF_
3
c1l9uH_
4
c1ku2A_
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d1siga_
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c1rp3G_
7
d1ku2a2
8
d1smyf3
9
d1rp3a3
10
c3t72o_
11
d1smyf2
12
d1ku7a_
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d2p7vb1
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d1ttya_
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c1or7A_
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c3mzyA_
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d1ku3a_
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c2q1zA_
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d1ku2a1
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d1l0oc_
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c1ciiA_
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c2k6xA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3iydF_
100.0 96 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
2c2a6eF_
100.0 59 PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
3c1l9uH_
100.0 56 PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution
4c1ku2A_
100.0 60 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
5d1siga_
100.0 86 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
6c1rp3G_
100.0 25 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
7d1ku2a2
100.0 60 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
8d1smyf3
100.0 60 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
9d1rp3a3
99.8 28 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
10c3t72o_
99.7 95 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
11d1smyf2
99.7 56 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
12d1ku7a_
99.6 56 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
13d2p7vb1
99.6 100 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
14d1ttya_
99.5 62 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
15c1or7A_
99.4 22 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
16c3mzyA_
99.4 31 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
17d1ku3a_
99.4 56 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
18c2q1zA_
99.3 20 PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
19d1ku2a1
99.2 59 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
20d1l0oc_
98.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
21c1l0oC_
not modelled 98.9 18 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
22d1rp3a2
not modelled 98.9 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
23c3hugA_
not modelled 98.8 19 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
24d1rp3a1
not modelled 98.7 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
25d1or7a1
not modelled 98.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
26c2o8xA_
not modelled 98.2 15 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
27d1xsva_
not modelled 98.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
28d1s7oa_
not modelled 98.1 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
29c1c1gA_
not modelled 98.0 8 PDB header:contractile protein
Chain: A: PDB Molecule:tropomyosin;
PDBTitle: crystal structure of tropomyosin at 7 angstroms resolution2 in the spermine-induced crystal form
30c1ciiA_
97.9 12 PDB header:transmembrane protein
Chain: A: PDB Molecule:colicin ia;
PDBTitle: colicin ia
31d1or7b2
not modelled 97.8 23 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
32d1or7a2
not modelled 97.8 21 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
33d1yioa1
not modelled 97.7 14 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)
34c3ojaB_
not modelled 97.4 13 PDB header:protein binding
Chain: B: PDB Molecule:anopheles plasmodium-responsive leucine-rich repeat protein
PDBTitle: crystal structure of lrim1/apl1c complex
35c1x3uA_
not modelled 97.2 18 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
36c2k6xA_
97.1 28 PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: autoregulation of a group 1 bacterial sigma factor involves2 the formation of a region 1.1- induced compacted structure
37c1yvlB_
not modelled 97.0 7 PDB header:signaling protein
Chain: B: PDB Molecule:signal transducer and activator of transcription
PDBTitle: structure of unphosphorylated stat1
38c1zljE_
not modelled 97.0 18 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
39c3qp5C_
not modelled 97.0 24 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
40d1a04a1
not modelled 97.0 21 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)
41c2o7gA_
not modelled 96.9 17 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
42c2rnjA_
not modelled 96.9 22 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
43d1fsea_
not modelled 96.8 29 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)
44c2krfB_
not modelled 96.8 22 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
45c2q0oA_
not modelled 96.8 19 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
46d1l3la1
not modelled 96.7 27 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)
47c3sztB_
not modelled 96.7 26 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
48c1h0mD_
not modelled 96.7 26 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
49d1p4wa_
not modelled 96.5 22 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)
50c3cloC_
not modelled 96.5 21 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
51c2w48D_
not modelled 96.0 15 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
52c3cwgA_
not modelled 95.9 8 PDB header:transcription
Chain: A: PDB Molecule:signal transducer and activator of transcription
PDBTitle: unphosphorylated mouse stat3 core fragment
53c3n0rA_
not modelled 95.5 19 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: structure of the phyr stress response regulator at 1.25 angstrom2 resolution
54d1h3la_
not modelled 95.5 16 Fold:Sigma2 domain of RNA polymerase sigma factors
Superfamily:Sigma2 domain of RNA polymerase sigma factors
Family:Sigma2 domain of RNA polymerase sigma factors
55c3klnC_
not modelled 95.4 17 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
56c3c3wB_
not modelled 95.4 20 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
57c1bg1A_
not modelled 95.4 8 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (transcription factor stat3b);
PDBTitle: transcription factor stat3b/dna complex
58c2jpcA_
not modelled 95.3 22 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
59c1ei3C_
not modelled 94.9 4 PDB header:
PDB COMPND:
60c1bf5A_
not modelled 94.6 7 PDB header:gene regulation/dna
Chain: A: PDB Molecule:signal transducer and activator of transcription
PDBTitle: tyrosine phosphorylated stat-1/dna complex
61c2efrB_
not modelled 94.5 12 PDB header:contractile protein
Chain: B: PDB Molecule:general control protein gcn4 and tropomyosin 1 alpha chain;
PDBTitle: crystal structure of the c-terminal tropomyosin fragment with n- and2 c-terminal extensions of the leucine zipper at 1.8 angstroms3 resolution
62c1hciB_
not modelled 94.3 9 PDB header:triple-helix coiled coil
Chain: B: PDB Molecule:alpha-actinin 2;
PDBTitle: crystal structure of the rod domain of alpha-actinin
63c1deqF_
not modelled 94.3 9 PDB header:
PDB COMPND:
64c1zn2A_
not modelled 94.1 13 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
65c1rnlA_
not modelled 93.7 22 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
66c3na7A_
not modelled 93.6 9 PDB header:gene regulation, chaperone
Chain: A: PDB Molecule:hp0958;
PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874
67c2oevA_
not modelled 93.3 8 PDB header:protein transport
Chain: A: PDB Molecule:programmed cell death 6-interacting protein;
PDBTitle: crystal structure of alix/aip1
68d1jhfa1
not modelled 92.9 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
69c1u78A_
not modelled 92.9 22 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
70c2d3eD_
not modelled 92.7 15 PDB header:contractile protein
Chain: D: PDB Molecule:general control protein gcn4 and tropomyosin 1
PDBTitle: crystal structure of the c-terminal fragment of rabbit2 skeletal alpha-tropomyosin
71c1jchC_
not modelled 92.3 11 PDB header:ribosome inhibitor, hydrolase
Chain: C: PDB Molecule:colicin e3;
PDBTitle: crystal structure of colicin e3 in complex with its immunity protein
72d2o38a1
not modelled 92.0 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
73c2o38A_
not modelled 92.0 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: putative xre family transcriptional regulator
74c2v71A_
not modelled 91.3 10 PDB header:nuclear protein
Chain: A: PDB Molecule:nuclear distribution protein nude-like 1;
PDBTitle: coiled-coil region of nudel
75c3f2hA_
not modelled 91.2 24 PDB header:lyase
Chain: A: PDB Molecule:alkylmercury lyase;
PDBTitle: crystal structure of the mercury-bound form of merb mutant2 c160s, the organomercurial lyase involved in a bacterial3 mercury resistance system
76c3mkyP_
not modelled 89.9 16 PDB header:dna binding protein/dna
Chain: P: PDB Molecule:protein sopb;
PDBTitle: structure of sopb(155-323)-18mer dna complex, i23 form
77d2a6ca1
not modelled 89.9 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
78d1trra_
not modelled 89.8 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
79c1deqO_
not modelled 89.7 10 PDB header:
PDB COMPND:
80c3r0aB_
not modelled 89.2 11 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
81c3ghgK_
not modelled 88.8 4 PDB header:blood clotting
Chain: K: PDB Molecule:fibrinogen beta chain;
PDBTitle: crystal structure of human fibrinogen
82d2d1ha1
not modelled 88.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
83c2x4hA_
not modelled 88.7 15 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
84c3ojaA_
not modelled 88.3 13 PDB header:protein binding
Chain: A: PDB Molecule:leucine-rich immune molecule 1;
PDBTitle: crystal structure of lrim1/apl1c complex
85c1ei3E_
not modelled 88.0 5 PDB header:
PDB COMPND:
86c1deqD_
not modelled 87.8 5 PDB header:
PDB COMPND:
87c3hnwB_
not modelled 87.5 8 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a basic coiled-coil protein of unknown function2 from eubacterium eligens atcc 27750
88c3fmyA_
not modelled 87.4 13 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)
89d1vz0a1
not modelled 87.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
90c2w7nA_
not modelled 87.0 9 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
91c2bnoA_
not modelled 86.9 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:epoxidase;
PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
92c3mlfC_
not modelled 86.7 26 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: putative transcriptional regulator from staphylococcus aureus.
93d1rioa_
not modelled 86.6 8 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
94c3k2zA_
not modelled 85.7 19 PDB header:hydrolase
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: crystal structure of a lexa protein from thermotoga maritima
95c1y9qA_
not modelled 85.5 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
96c3dtpA_
not modelled 85.3 11 PDB header:contractile protein
Chain: A: PDB Molecule:myosin 2 heavy chain chimera of smooth and
PDBTitle: tarantula heavy meromyosin obtained by flexible docking to2 tarantula muscle thick filament cryo-em 3d-map
97d2cfxa1
not modelled 85.0 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
98c2p6tH_
not modelled 85.0 16 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
99c3kxaD_
not modelled 83.9 20 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae
100d2cg4a1
not modelled 83.7 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
101d1biaa1
not modelled 83.6 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
102c2l4aA_
not modelled 83.4 11 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
103d1nr3a_
not modelled 83.4 19 Fold:DNA-binding protein Tfx
Superfamily:DNA-binding protein Tfx
Family:DNA-binding protein Tfx
104d2b5aa1
not modelled 83.3 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
105d1i1ga1
not modelled 83.1 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
106c2it0A_
not modelled 83.1 13 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
107c3nqoB_
not modelled 83.0 13 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
108c2jvlA_
not modelled 82.8 25 PDB header:transcription
Chain: A: PDB Molecule:trmbf1;
PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
109c3trbA_
not modelled 82.8 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
110d1r71a_
not modelled 82.7 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
111d1y7ya1
not modelled 82.6 12 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
112c2ef8A_
not modelled 82.6 15 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcription factor;
PDBTitle: crystal structure of c.ecot38is
113d1lmb3_
not modelled 82.4 9 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
114c2vbzA_
not modelled 82.0 14 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
115d1jhga_
not modelled 81.7 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
116c3f6wE_
not modelled 81.6 15 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
117c1r71B_
not modelled 81.6 21 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
118c2gl2B_
not modelled 81.5 11 PDB header:cell adhesion
Chain: B: PDB Molecule:adhesion a;
PDBTitle: crystal structure of the tetra muntant (t66g,r67g,f68g,2 y69g) of bacterial adhesin fada
119c2ppxA_
not modelled 81.3 19 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
120d2ppxa1
not modelled 81.3 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like

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