Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP31062
DateThu Jan 5 11:46:59 GMT 2012
Unique Job IDfe19f50d71ff2b31

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1j9ia_
Top template information
Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:Terminase gpNU1 subunit domain
Confidence and coverage
Confidence: 99.5% Coverage: 38%
68 residues ( 38% of your sequence) have been modelled with 99.5% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
147 residues ( 81%) 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  MEVNKKQLADIFGASIRTIQNWQEQGMPVLRGGGKGNEVLYDSAAVIKWYAERDAEIENE
Secondary structure 























SS confidence 



























































Disorder  ????























?????























???
Disorder confidence 



























































 
   .........70.........80.........90.........100.........110.........120
Sequence  KLRREVEELLQASETDLQPGTIEYERHRLTRAQADAQELKNARDSAEVVETAFCTFVLSR
Secondary structure 














SS confidence 



























































Disorder  ??????



????????????





















?














Disorder confidence 



























































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














SS confidence 



























































Disorder 








???






























???
??







???
Disorder confidence 



























































 
   .
Sequence  G
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 1j9i chain A

3D model

Region: 1 - 68
Aligned: 68
Modelled: 68
Confidence: 99.5%
Identity: 100%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: Terminase gpNU1 subunit domain

Phyre2

PDB 3hh0 chain C

3D model

Region: 1 - 179
Aligned: 125
Modelled: 125
Confidence: 97.1%
Identity: 12%
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 1r8d chain A

3D model

Region: 1 - 48
Aligned: 48
Modelled: 48
Confidence: 96.9%
Identity: 27%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2

PDB 1q06 chain A

3D model

Region: 3 - 105
Aligned: 103
Modelled: 103
Confidence: 96.8%
Identity: 13%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2

PDB 3qao chain A

3D model

Region: 3 - 48
Aligned: 46
Modelled: 45
Confidence: 96.2%
Identity: 26%
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: 3 - 36
Aligned: 34
Modelled: 34
Confidence: 96.2%
Identity: 9%
PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr

Phyre2

PDB 3gp4 chain B

3D model

Region: 3 - 48
Aligned: 46
Modelled: 46
Confidence: 96.1%
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 2vz4 chain A

3D model

Region: 3 - 48
Aligned: 46
Modelled: 46
Confidence: 96.1%
Identity: 20%
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 1r8e chain A domain 1

3D model

Region: 4 - 160
Aligned: 108
Modelled: 108
Confidence: 96.0%
Identity: 13%
Fold: Putative DNA-binding domain
Superfamily: Putative DNA-binding domain
Family: DNA-binding N-terminal domain of transcription activators

Phyre2

PDB 3bd1 chain B

3D model

Region: 4 - 32
Aligned: 29
Modelled: 29
Confidence: 95.8%
Identity: 24%
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

Phyre2

PDB 2jml chain A

3D model

Region: 1 - 48
Aligned: 48
Modelled: 48
Confidence: 95.7%
Identity: 21%
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 2ppx chain A domain 1

3D model

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 95.6%
Identity: 7%
Fold: lambda repressor-like DNA-binding domains
Superfamily: lambda repressor-like DNA-binding domains
Family: SinR domain-like

Phyre2

PDB 2ppx chain A

3D model

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 95.6%
Identity: 7%
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

Phyre2

PDB 3gpv chain A

3D model

Region: 4 - 48
Aligned: 45
Modelled: 45
Confidence: 95.6%
Identity: 16%
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 2fjr chain B

3D model

Region: 4 - 29
Aligned: 26
Modelled: 26
Confidence: 95.3%
Identity: 27%
PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186

Phyre2

PDB 3fmy chain A

3D model

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 95.2%
Identity: 17%
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)

Phyre2

PDB 3gn5 chain B

3D model

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 94.4%
Identity: 17%
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)

Phyre2

PDB 1bia chain A domain 1

3D model

Region: 3 - 36
Aligned: 34
Modelled: 34
Confidence: 93.7%
Identity: 29%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Biotin repressor-like

Phyre2

PDB 2eby chain A

3D model

Region: 1 - 29
Aligned: 29
Modelled: 29
Confidence: 93.7%
Identity: 7%
PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli

Phyre2

PDB 2kpj chain A

3D model

Region: 2 - 29
Aligned: 28
Modelled: 28
Confidence: 93.5%
Identity: 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

Phyre2
1

d1j9ia_
2

c3hh0C_
3

d1r8da_
4

d1q06a_
5

c3qaoA_
6

c2zhhA_
7

c3gp4B_
8

c2vz4A_
9

d1r8ea1
10

c3bd1B_
11

c2jmlA_
12

d2ppxa1
13

c2ppxA_
14

c3gpvA_
15

c2fjrB_
16

c3fmyA_
17

c3gn5B_
18

d1biaa1
19

c2ebyA_
20

c2kpjA_
21



22



23



24



25



26



27



28



29



30



31



32



33



34



35



36



37



38



39



40



41



42



43



44



45



46



47



48



49



50



51



52



53



54



55



56



57



58



59



60



61



62



63



64



65



66



67



68



69



70



71



72



73



74



75



76



77



78



79



80



81



82



83



84



85



86



87



88



89



90



91



92



93



94



95



96



97



98



99



100



101



102



103



104



105



106



107



108



109



110



111



112



113



114



115



116



117



118



119



120



121



122



123



124



125



126



127



128



129



130



131



132



133



134



135



136



137



138



139



140



141



142



143



144



145



146



147



148



149



150



151



152



153



154



155



156



157



158



159



160



161



162



163



164



165



166



167



168



169



170



171



172



173



174



175



176



177



178



179



180



181



182



183



184



185



186



187



188



189



190



191



192



193



194



195



196



197



198



199



200



201



202



203



204



205



206



207



208



209



210



211



212



213



214



215



216



217



218



219



220



221



222



223



224



225



226



227



228



229



230



231



232



233



234



235



236



237



238



239



240



241



242



243



244



245



246



247



248



249



250



251



252



253



254



255



256



257



258



259



260



261



262



263



264



265



266



267



268



269



270



271



272



273



274



275



276



277



278



279



280



281



282



283



284



285



286



287



288



289



290



291



292



293



294



295



296



297



298



299



300



301



302



303



304



305



306



307



308



309



310



311



312



313



314



315



316



317



318



319



320



321



322



323



324



325



326



327



328



329



330



331



332



333



334



335



336



337



338



339



340



341



342



343



344



345



346



347



348



349



350



351



352



353



354



355



356



357



358



359



360



361



362



363



364



365



366



367



368



369



370



371



372



373



374



375



376



377



378



379



380



381



382



383



384



385



386



387



388



389



390



391



392



393



394



395



396



397



398



399



400



401



402



403



404



405



406



407



408



409



410



411



412



413



414



415



416



417



418



419



420



421



422



423



424



425



426



427



428



429



430



431



432



433



434



435



436



437



438



439



440



441



442



443



444



445



446



447



448



449



450



451



452



453



454



455



456



457



458



459



460



461



462



463



464



465



466



467



468



469



470



471



472



473



474



475



476



477



478



479



480



481



482



483



484



485



486



487



488



489



490



491



492



493



494



495



496



497



498






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1j9ia_



99.5 100 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:Terminase gpNU1 subunit domain
2c3hh0C_



97.1 12 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus
3d1r8da_



96.9 27 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
4d1q06a_



96.8 13 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
5c3qaoA_



96.2 26 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
6c2zhhA_



96.2 9 PDB header:transcription
Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr;
PDBTitle: crystal structure of soxr
7c3gp4B_



96.1 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
8c2vz4A_



96.1 20 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
9d1r8ea1



96.0 13 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
10c3bd1B_



95.8 24 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
11c2jmlA_



95.7 21 PDB header:transcription
Chain: A: PDB Molecule:dna binding domain/transcriptional regulator;
PDBTitle: solution structure of the n-terminal domain of cara repressor
12d2ppxa1



95.6 7 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
13c2ppxA_



95.6 7 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
14c3gpvA_



95.6 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, merr family;
PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis
15c2fjrB_



95.3 27 PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186
16c3fmyA_



95.2 17 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)
17c3gn5B_



94.4 17 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)
18d1biaa1



93.7 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
19c2ebyA_



93.7 7 PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli
20c2kpjA_



93.5 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
21d2croa_



not modelled 93.4 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
22c2xcjB_



not modelled 93.4 21 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
23d1r69a_



not modelled 93.2 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
24d1sq8a_



not modelled 93.2 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
25c3omtA_



not modelled 93.1 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae.
26c1z4hA_



not modelled 93.0 9 PDB header:protein binding, dna binding protein
Chain: A: PDB Molecule:tor inhibition protein;
PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase
27c3op9A_



not modelled 92.9 14 PDB header:transcription regulator
Chain: A: PDB Molecule:pli0006 protein;
PDBTitle: crystal structure of transcriptional regulator from listeria innocua
28c3mlfC_



not modelled 92.8 34 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: putative transcriptional regulator from staphylococcus aureus.
29c2jvlA_



not modelled 92.8 11 PDB header:transcription
Chain: A: PDB Molecule:trmbf1;
PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei
30c1u78A_



not modelled 92.7 8 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
31c1zvvA_



not modelled 92.6 20 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
32c3bs3A_



not modelled 92.5 24 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
33d1x57a1



not modelled 92.3 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:EDF1-like
34d1i5za1



not modelled 92.3 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
35c2kfsA_



not modelled 92.3 15 PDB header:dna-binding protein
Chain: A: PDB Molecule:conserved hypothetical regulatory protein;
PDBTitle: nmr structure of rv2175c
36d1ft9a1



not modelled 92.1 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
37d1llib_



not modelled 92.0 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
38c3cecA_



not modelled 91.9 28 PDB header:transcription
Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system;
PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution
39c3trbA_



not modelled 91.8 10 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
40d2h6ca1



not modelled 91.7 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
41c2w48D_



not modelled 91.6 21 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
42d1rzsa_



not modelled 91.6 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
43d2icta1



not modelled 91.1 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
44d2oz6a1



not modelled 91.1 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
45d1b0na2



not modelled 90.9 12 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
46c3dnvB_



not modelled 90.9 24 PDB header:transcription/dna
Chain: B: PDB Molecule:hth-type transcriptional regulator hipb;
PDBTitle: mdt protein
47d1hlva1



not modelled 90.9 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
48c3ivpD_



not modelled 90.8 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.
49c2ef8A_



not modelled 90.8 17 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcription factor;
PDBTitle: crystal structure of c.ecot38is
50c3f52A_



not modelled 90.8 18 PDB header:transcription activator
Chain: A: PDB Molecule:clp gene regulator (clgr);
PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum
51d3e5ua1



not modelled 90.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
52c2dg6A_



not modelled 90.6 34 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)
53c3d6zA_



not modelled 90.6 6 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
54d1j5ya1



not modelled 90.6 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
55d2a6ca1



not modelled 90.6 8 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
56d2coha1



not modelled 90.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
57c1b0nA_



not modelled 90.6 12 PDB header:transcription regulator
Chain: A: PDB Molecule:protein (sinr protein);
PDBTitle: sinr protein/sini protein complex
58d1lmb3_



not modelled 90.5 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
59d1rioa_



not modelled 90.5 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
60d1ic8a2



not modelled 90.2 19 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:POU-specific domain
61d2gaua1



not modelled 90.2 10 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
62c2o38A_



not modelled 90.0 8 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: putative xre family transcriptional regulator
63d2o38a1



not modelled 90.0 8 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE1354
64d1k78a1



not modelled 89.9 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
65d1adra_



not modelled 89.9 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
66d2r1jl1



not modelled 89.9 18 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
67c3t76A_



not modelled 89.8 18 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator vanug;
PDBTitle: crystal structure of transcriptional regulator vanug, form ii
68d1y9qa1



not modelled 89.7 11 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Probable transcriptional regulator VC1968, N-terminal domain
69d2bgca1



not modelled 89.7 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
70c1y9qA_



not modelled 89.6 11 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
71c6paxA_



not modelled 89.6 8 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
72d2b5aa1



not modelled 89.5 21 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
73d1pdnc_



not modelled 89.3 4 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
74c3kxaD_



not modelled 89.2 11 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae
75c3bwgA_



not modelled 89.2 21 PDB header:transcription regulator
Chain: A: PDB Molecule:uncharacterized hth-type transcriptional regulator yydk;
PDBTitle: the crystal structure of possible transcriptional regulator yydk from2 bacillus subtilis subsp. subtilis str. 168
76c2elhA_



not modelled 89.0 21 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
77c3clcC_



not modelled 89.0 11 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
78c1hlvA_



not modelled 88.7 17 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:major centromere autoantigen b;
PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna
79d6paxa1



not modelled 88.6 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
80d1utxa_



not modelled 88.6 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
81c3neuA_



not modelled 88.6 9 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin1836 protein;
PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
82d2jn6a1



not modelled 88.4 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
83c3f8mA_



not modelled 88.3 19 PDB header:transcription
Chain: A: PDB Molecule:gntr-family protein transcriptional regulator;
PDBTitle: crystal structure of phnf from mycobacterium smegmatis
84c3b7hA_



not modelled 88.3 17 PDB header:structural protein
Chain: A: PDB Molecule:prophage lp1 protein 11;
PDBTitle: crystal structure of the prophage lp1 protein 11
85c3eusB_



not modelled 88.1 7 PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding protein;
PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi
86c2du9A_



not modelled 88.0 24 PDB header:transcription
Chain: A: PDB Molecule:predicted transcriptional regulators;
PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
87c3by6C_



not modelled 88.0 12 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
88c3eetA_



not modelled 88.0 17 PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
89c2di3A_



not modelled 87.9 15 PDB header:transcription
Chain: A: PDB Molecule:bacterial regulatory proteins, gntr family;
PDBTitle: crystal structure of the transcriptional factor cgl29152 from corynebacterium glutamicum
90d1y7ya1



not modelled 87.9 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
91c3fmsA_



not modelled 87.6 13 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of tm0439, a gntr transcriptional2 regulator
92d1bw6a_



not modelled 87.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
93d1pm6a_



not modelled 87.2 17 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:Excisionase-like
94c2ewtA_



not modelled 86.9 7 PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna-binding protein;
PDBTitle: crystal structure of the dna-binding domain of bldd
95c3edpB_



not modelled 86.8 32 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:lin2111 protein;
PDBTitle: the crystal structure of the protein lin2111 (functionally unknown)2 from listeria innocua clip11262
96c2hs5A_



not modelled 86.3 9 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcriptional regulator gntr;
PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator gntr from rhodococcus sp. rha1
97c2bgcA_



not modelled 86.1 15 PDB header:transcription
Chain: A: PDB Molecule:prfa;
PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes
98c3f6wE_



not modelled 86.0 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
99d1hw1a1



not modelled 86.0 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
100d3ctaa1



not modelled 85.6 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
101d2p7vb1



not modelled 85.4 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
102c3kjxD_



not modelled 85.3 15 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
103d2ofya1



not modelled 85.3 17 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
104c3c7jA_



not modelled 85.2 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, gntr family;
PDBTitle: crystal structure of transcriptional regulator (gntr family member)2 from pseudomonas syringae pv. tomato str. dc3000
105d1lcda_



not modelled 84.8 28 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
106d1xsva_



not modelled 84.6 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
107d1rp3a2



not modelled 84.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
108c2o8xA_



not modelled 84.3 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
109d1z6ra1



not modelled 84.3 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
110d1stza1



not modelled 84.3 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
111d2isya1



not modelled 84.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
112c1e2xA_



not modelled 84.0 15 PDB header:transcriptional regulation
Chain: A: PDB Molecule:fatty acid metabolism regulator protein;
PDBTitle: fadr, fatty acid responsive transcription factor from e.2 coli
113d1g3wa1



not modelled 83.9 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
114d2ao9a1



not modelled 83.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Nanomeric phage protein-like
115c1j5yA_



not modelled 83.8 32 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family;
PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution
116d3bwga1



not modelled 83.6 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
117d1ku7a_



not modelled 83.4 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
118c3mkyP_



not modelled 83.4 12 PDB header:dna binding protein/dna
Chain: P: PDB Molecule:protein sopb;
PDBTitle: structure of sopb(155-323)-18mer dna complex, i23 form
119d1z05a1



not modelled 83.3 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
120c2bnoA_



not modelled 83.3 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:epoxidase;
PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.

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