Secondary structure and disorder prediction

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10

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20

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30

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40

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50

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60

Sequence

M

N

T

V

F

L

H

L

S

E

E

A

I

K

R

L

N

K

L

R

G

W

R

K

V

S

R

S

A

I

L

R

E

A

V

E

Q

Y

L

E

R

Q

Q

F

P

V

R

K

A

K

G

G

R

Q

K

G

E

V

V

G

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

Sequence

V

D

D

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C

K

E

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K

E

Secondary structure

SS confidence

Disorder

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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

Rank Aligned region

PDB 2k5j chain B Region: 1 - 70 Aligned: 70 Modelled: 70 Confidence: 100.0% Identity: 41% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein yiif; PDBTitle: solution structure of protein yiif from shigella flexneri2 serotype 5b (strain 8401) . northeast structural genomics3 consortium target sft1 Phyre2 PDB 1q5v chain B Region: 1 - 49 Aligned: 49 Modelled: 49 Confidence: 97.9% Identity: 20% PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr Phyre2 PDB 2bj3 chain D Region: 1 - 52 Aligned: 52 Modelled: 52 Confidence: 97.9% Identity: 12% PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo Phyre2 PDB 2bj7 chain A domain 1 Region: 1 - 45 Aligned: 45 Modelled: 45 Confidence: 97.9% Identity: 9% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2ca9 chain B Region: 1 - 42 Aligned: 42 Modelled: 42 Confidence: 97.7% Identity: 17% PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation Phyre2 PDB 2hza chain A domain 1 Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 97.1% Identity: 23% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2hza chain B domain 1 Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 96.9% Identity: 23% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2rbf chain B Region: 2 - 41 Aligned: 40 Modelled: 40 Confidence: 94.9% Identity: 18% PDB header:oxidoreductase/dna Chain: B: PDB Molecule:bifunctional protein puta; PDBTitle: structure of the ribbon-helix-helix domain of escherichia coli puta2 (puta52) complexed with operator dna (o2) Phyre2 PDB 2cpg chain A Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 93.9% Identity: 30% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2an7 chain A Region: 1 - 45 Aligned: 37 Modelled: 45 Confidence: 91.6% Identity: 19% PDB header:dna binding protein Chain: A: PDB Molecule:protein pard; PDBTitle: solution structure of the bacterial antidote pard Phyre2 PDB 2k9i chain B Region: 4 - 47 Aligned: 44 Modelled: 44 Confidence: 89.0% Identity: 18% PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus Phyre2 PDB 3h87 chain D Region: 7 - 69 Aligned: 63 Modelled: 63 Confidence: 88.8% Identity: 19% PDB header:toxin/antitoxin Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis Phyre2 PDB 2ay0 chain A domain 1 Region: 2 - 41 Aligned: 40 Modelled: 40 Confidence: 79.1% Identity: 18% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: PutA pre-N-terminal region-like Phyre2 PDB 2bsq chain E domain 1 Region: 7 - 41 Aligned: 35 Modelled: 35 Confidence: 52.1% Identity: 17% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Trafficking protein A-like Phyre2 PDB 2k29 chain A Region: 1 - 45 Aligned: 45 Modelled: 45 Confidence: 49.6% Identity: 22% PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb Phyre2 PDB 1p94 chain A Region: 3 - 42 Aligned: 40 Modelled: 40 Confidence: 43.2% Identity: 18% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2q2k chain A Region: 14 - 40 Aligned: 27 Modelled: 27 Confidence: 25.3% Identity: 26% PDB header:dna binding protein/dna Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of nucleic-acid binding protein Phyre2 PDB 1fcd chain C domain 1 Region: 1 - 46 Aligned: 27 Modelled: 27 Confidence: 22.4% Identity: 19% Fold: Cytochrome c Superfamily: Cytochrome c Family: Two-domain cytochrome c Phyre2 PDB 1yxe chain A Region: 44 - 56 Aligned: 13 Modelled: 13 Confidence: 21.2% Identity: 23% PDB header:immune system Chain: A: PDB Molecule:apical membrane antigen 1; PDBTitle: structure and inter-domain interactions of domain ii from the blood2 stage malarial protein, apical membrane antigen 1 Phyre2 PDB 2kel chain B Region: 6 - 41 Aligned: 36 Modelled: 36 Confidence: 20.4% Identity: 17% PDB header:transcription repressor Chain: B: PDB Molecule:uncharacterized protein 56b; PDBTitle: structure of the transcription regulator svtr from the2 hyperthermophilic archaeal virus sirv1 Phyre2 1 c2k5jB_ 2 c1q5vB_ 3 c2bj3D_ 4 d2bj7a1 5 c2ca9B_ 6 d2hzaa1 7 d2hzab1 8 c2rbfB_ 9 d2cpga_ 10 c2an7A_ 11 c2k9iB_ 12 c3h87D_ 13 d2ay0a1 14 d2bsqe1 15 c2k29A_ 16 d1p94a_ 17 c2q2kA_ 18 d1fcdc1 19 c1yxeA_ 20 c2kelB_ 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

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2k5jB_ 100.0 41 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein yiif; PDBTitle: solution structure of protein yiif from shigella flexneri2 serotype 5b (strain 8401) . northeast structural genomics3 consortium target sft1 2 c1q5vB_ 97.9 20 PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr 3 c2bj3D_ 97.9 12 PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo 4 d2bj7a1 97.9 9 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 5 c2ca9B_ 97.7 17 PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation 6 d2hzaa1 97.1 23 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 7 d2hzab1 96.9 23 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 8 c2rbfB_ 94.9 18 PDB header:oxidoreductase/dna Chain: B: PDB Molecule:bifunctional protein puta; PDBTitle: structure of the ribbon-helix-helix domain of escherichia coli puta2 (puta52) complexed with operator dna (o2) 9 d2cpga_ 93.9 30 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 10 c2an7A_ 91.6 19 PDB header:dna binding protein Chain: A: PDB Molecule:protein pard; PDBTitle: solution structure of the bacterial antidote pard 11 c2k9iB_ 89.0 18 PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus 12 c3h87D_ 88.8 19 PDB header:toxin/antitoxin Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis 13 d2ay0a1 79.1 18 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:PutA pre-N-terminal region-like 14 d2bsqe1 52.1 17 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Trafficking protein A-like 15 c2k29A_ 49.6 22 PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb 16 d1p94a_ 43.2 18 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 17 c2q2kA_ 25.3 26 PDB header:dna binding protein/dna Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of nucleic-acid binding protein 18 d1fcdc1 22.4 19 Fold:Cytochrome c Superfamily:Cytochrome c Family:Two-domain cytochrome c 19 c1yxeA_ 21.2 23 PDB header:immune system Chain: A: PDB Molecule:apical membrane antigen 1; PDBTitle: structure and inter-domain interactions of domain ii from the blood2 stage malarial protein, apical membrane antigen 1 20 c2kelB_ 20.4 17 PDB header:transcription repressor Chain: B: PDB Molecule:uncharacterized protein 56b; PDBTitle: structure of the transcription regulator svtr from the2 hyperthermophilic archaeal virus sirv1 21 c3kxeD_ not modelled 20.3 13 PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex 22 d1mnta_ not modelled 18.6 15 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 23 c2dbiA_ not modelled 18.5 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ybiu; PDBTitle: crystal structure of a hypothetical protein jw0805 from2 escherichia coli 24 c3mayE_ not modelled 16.1 7 PDB header:heme-binding protein Chain: E: PDB Molecule:possible exported protein; PDBTitle: crystal structure of a secreted mycobacterium tuberculosis heme-2 binding protein 25 c2qhoF_ not modelled 15.2 30 PDB header:protein binding/ligase Chain: F: PDB Molecule:e3 ubiquitin-protein ligase edd1; PDBTitle: crystal structure of the uba domain from edd ubiquitin2 ligase in complex with ubiquitin 26 c3o39A_ not modelled 13.7 16 PDB header:chaperone Chain: A: PDB Molecule:periplasmic protein related to spheroblast formation; PDBTitle: crystal structure of spy 27 d1i27a_ not modelled 13.0 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of the rap74 subunit of TFIIF 28 c1ny9A_ not modelled 11.0 22 PDB header:transcription Chain: A: PDB Molecule:transcriptional activator tipa-s; PDBTitle: antibiotic binding domain of a tipa-class multidrug2 resistance transcriptional regulator 29 d1ny9a_ not modelled 11.0 22 Fold:Antibiotic binding domain of TipA-like multidrug resistance regulators Superfamily:Antibiotic binding domain of TipA-like multidrug resistance regulators Family:Antibiotic binding domain of TipA-like multidrug resistance regulators 30 d1l5aa2 not modelled 10.2 20 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:NRPS condensation domain (amide synthase) 31 c3qzcA_ not modelled 9.8 12 PDB header:signaling protein Chain: A: PDB Molecule:periplasmic protein cpxp; PDBTitle: structure of the periplasmic stress response protein cpxp 32 c2rqpA_ not modelled 9.7 15 PDB header:gene regulation Chain: A: PDB Molecule:heterochromatin protein 1-binding protein 3; PDBTitle: the solution structure of heterochromatin protein 1-binding2 protein 74 histone h1 like domain 33 d1b3ta_ not modelled 9.3 14 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 34 d1vhib_ not modelled 9.2 14 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 35 c3oeoD_ not modelled 8.7 13 PDB header:signaling protein Chain: D: PDB Molecule:spheroplast protein y; PDBTitle: the crystal structure e. coli spy 36 d1fcdc2 not modelled 8.6 4 Fold:Cytochrome c Superfamily:Cytochrome c Family:Two-domain cytochrome c 37 c2hwyB_ not modelled 8.3 14 PDB header:rna binding protein Chain: B: PDB Molecule:protein smg5; PDBTitle: structure of pin domain of human smg5. 38 c1kcfB_ not modelled 8.3 22 PDB header:hydrolase Chain: B: PDB Molecule:hypothetical 30.2 kd protein c25g10.02 in PDBTitle: crystal structure of the yeast mitochondrial holliday2 junction resolvase, ydc2 39 c2fu2A_ not modelled 8.0 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein spy2152; PDBTitle: crystal structure of protein spy2152 from streptococcus pyogenes 40 c1sfeA_ not modelled 7.9 12 PDB header:dna-binding protein Chain: A: PDB Molecule:ada o6-methylguanine-dna methyltransferase; PDBTitle: ada o6-methylguanine-dna methyltransferase from escherichia coli 41 c1x93B_ not modelled 7.7 21 PDB header:transcription Chain: B: PDB Molecule:hypothetical protein hp0222; PDBTitle: nmr structure of helicobacter pylori hp0222 42 d1x93a1 not modelled 7.7 21 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 43 d2phcb1 not modelled 7.0 6 Fold:Cyclophilin-like Superfamily:Cyclophilin-like Family:PH0987 C-terminal domain-like 44 d2outa2 not modelled 7.0 21 Fold:GINS/PriA/YqbF domain Superfamily:PriA/YqbF domain Family:YqbF N-terminal domain-like 45 c3g5oC_ not modelled 6.8 23 PDB header:toxin/antitoxin Chain: C: PDB Molecule:uncharacterized protein rv2866; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis 46 c3epvB_ not modelled 6.7 9 PDB header:metal binding protein Chain: B: PDB Molecule:nickel and cobalt resistance protein cnrr; PDBTitle: x-ray structure of the metal-sensor cnrx in both the apo- and copper-2 bound forms 47 d1uxca_ not modelled 6.3 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 48 c2e4jA_ not modelled 6.2 12 PDB header:isomerase Chain: A: PDB Molecule:prostaglandin-h2 d-isomerase; PDBTitle: solution structure of mouse lipocalin-type prostaglandin d2 synthase 49 d1yqaa1 not modelled 6.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Linker histone H1/H5 50 c3by0B_ not modelled 6.0 12 PDB header:ligand binding protein Chain: B: PDB Molecule:neutrophil gelatinase-associated lipocalin; PDBTitle: crystal structure of siderocalin (ngal, lipocalin 2) w79a-r81a2 complexed with ferric enterobactin 51 d1znda1 not modelled 6.0 24 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 52 c2o3fC_ not modelled 6.0 24 PDB header:transcription Chain: C: PDB Molecule:putative hth-type transcriptional regulator ybbh; PDBTitle: structural genomics, the crystal structure of the n-2 terminal domain of the putative transcriptional regulator3 ybbh from bacillus subtilis subsp. subtilis str. 168. 53 d2o3fa1 not modelled 6.0 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:RpiR-like 54 d2csga1 not modelled 5.8 13 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:YbiU-like 55 c3itfA_ not modelled 5.8 19 PDB header:signaling protein Chain: A: PDB Molecule:periplasmic adaptor protein cpxp; PDBTitle: structural basis for the inhibitory function of the cpxp adaptor2 protein 56 c2jobA_ not modelled 5.6 11 PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site 57 c2zqeA_ not modelled 5.6 33 PDB header:dna binding protein Chain: A: PDB Molecule:muts2 protein; PDBTitle: crystal structure of the smr domain of thermus thermophilus muts2 58 d1uhma_ not modelled 5.5 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Linker histone H1/H5 59 c2zp2B_ not modelled 5.4 12 PDB header:transferase inhibitor Chain: B: PDB Molecule:kinase a inhibitor; PDBTitle: c-terminal domain of kipi from bacillus subtilis 60 d2je6b2 not modelled 5.3 13 Fold:Ribonuclease PH domain 2-like Superfamily:Ribonuclease PH domain 2-like Family:Ribonuclease PH domain 2-like 61 c2lcvA_ not modelled 5.3 24 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional repressor cytr; PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation

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

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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