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

G

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F

N

F

V

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D

A

G

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K

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W

D

A

V

T

G

Q

H

D

K

D

D

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A

K

K

V

Q

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H

L

N

K

T

G

I

P

D

A

D

K

V

N

I

Q

I

A

D

G

K

A

T

V

T

G

D

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

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90

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100

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110

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120

Sequence

G

L

S

Q

E

A

K

E

K

I

L

V

A

V

G

N

I

S

G

I

A

S

V

D

D

Q

V

K

T

A

T

P

A

T

A

S

Q

F

Y

T

V

K

S

G

D

T

L

S

A

I

S

K

Q

V

Y

G

N

A

N

L

Secondary structure

SS confidence

Disorder

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Disorder confidence

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130

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140

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Sequence

Y

N

K

I

F

E

A

N

K

P

M

L

K

S

P

D

K

I

Y

P

G

Q

V

L

R

I

P

E

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 2l9y chain A Region: 85 - 149 Aligned: 60 Modelled: 62 Confidence: 99.6% Identity: 32% PDB header:sugar binding protein Chain: A: PDB Molecule:cvnh-lysm lectin; PDBTitle: solution structure of the mocvnh-lysm module from the rice blast2 fungus magnaporthe oryzae protein (mgg_03307) Phyre2 PDB 1e0g chain A Region: 95 - 149 Aligned: 48 Modelled: 55 Confidence: 99.5% Identity: 27% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2djp chain A Region: 84 - 147 Aligned: 59 Modelled: 64 Confidence: 99.5% Identity: 24% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein sb145; PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145 Phyre2 PDB 1y7m chain A domain 2 Region: 98 - 147 Aligned: 44 Modelled: 48 Confidence: 99.4% Identity: 34% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2gu1 chain A Region: 98 - 147 Aligned: 47 Modelled: 50 Confidence: 98.7% Identity: 36% PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae Phyre2 PDB 1y7m chain B Region: 98 - 130 Aligned: 30 Modelled: 33 Confidence: 98.1% Identity: 33% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein bsu14040; PDBTitle: crystal structure of the b. subtilis ykud protein at 2 a2 resolution Phyre2 PDB 2elh chain A Region: 101 - 126 Aligned: 26 Modelled: 26 Confidence: 34.9% Identity: 4% 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 Phyre2 PDB 1k78 chain A domain 1 Region: 101 - 141 Aligned: 37 Modelled: 41 Confidence: 26.3% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1y0p chain A domain 3 Region: 101 - 128 Aligned: 28 Modelled: 28 Confidence: 26.2% Identity: 14% Fold: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Phyre2 PDB 2r0q chain F Region: 103 - 129 Aligned: 27 Modelled: 27 Confidence: 21.4% Identity: 26% PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex Phyre2 PDB 2lfc chain A Region: 101 - 129 Aligned: 29 Modelled: 29 Confidence: 17.8% Identity: 10% PDB header:oxidoreductase Chain: A: PDB Molecule:fumarate reductase, flavoprotein subunit; PDBTitle: solution nmr structure of fumarate reductase flavoprotein subunit from2 lactobacillus plantarum, northeast structural genomics consortium3 target lpr145j Phyre2 PDB 2ofy chain A domain 1 Region: 105 - 126 Aligned: 19 Modelled: 22 Confidence: 16.2% Identity: 11% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: SinR domain-like Phyre2 PDB 1sig chain A Region: 108 - 126 Aligned: 19 Modelled: 19 Confidence: 15.2% Identity: 11% 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 2a6e chain F Region: 108 - 126 Aligned: 19 Modelled: 19 Confidence: 14.6% Identity: 16% PDB header:transferase Chain: F: PDB Molecule:rna polymerase sigma factor rpod; PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme Phyre2 PDB 1smy chain F domain 3 Region: 108 - 126 Aligned: 19 Modelled: 19 Confidence: 13.5% Identity: 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 Phyre2 PDB 1ku2 chain A domain 2 Region: 107 - 126 Aligned: 20 Modelled: 20 Confidence: 13.3% Identity: 15% 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 1iyj chain B domain 3 Region: 136 - 146 Aligned: 11 Modelled: 11 Confidence: 13.0% Identity: 18% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 1hlv chain A domain 1 Region: 101 - 126 Aligned: 26 Modelled: 26 Confidence: 12.8% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 2cx1 chain A domain 1 Region: 104 - 113 Aligned: 10 Modelled: 10 Confidence: 12.3% Identity: 30% Fold: PUA domain-like Superfamily: PUA domain-like Family: PUA domain Phyre2 PDB 1bxl chain A Region: 105 - 127 Aligned: 23 Modelled: 23 Confidence: 11.3% Identity: 4% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 1 c2l9yA_ 2 d1e0ga_ 3 c2djpA_ 4 d1y7ma2 5 c2gu1A_ 6 c1y7mB_ 7 c2elhA_ 8 d1k78a1 9 d1y0pa3 10 c2r0qF_ 11 c2lfcA_ 12 d2ofya1 13 d1siga_ 14 c2a6eF_ 15 d1smyf3 16 d1ku2a2 17 d1iyjb3 18 d1hlva1 19 d2cx1a1 20 d1bxla_ 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

Detailed template information

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

1 c2l9yA_ 99.6 32 PDB header:sugar binding protein Chain: A: PDB Molecule:cvnh-lysm lectin; PDBTitle: solution structure of the mocvnh-lysm module from the rice blast2 fungus magnaporthe oryzae protein (mgg_03307) 2 d1e0ga_ 99.5 27 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 3 c2djpA_ 99.5 24 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein sb145; PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145 4 d1y7ma2 99.4 34 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 5 c2gu1A_ 98.7 36 PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae 6 c1y7mB_ 98.1 33 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein bsu14040; PDBTitle: crystal structure of the b. subtilis ykud protein at 2 a2 resolution 7 c2elhA_ 34.9 4 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 8 d1k78a1 26.3 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 9 d1y0pa3 26.2 14 Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 10 c2r0qF_ 21.4 26 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 11 c2lfcA_ 17.8 10 PDB header:oxidoreductase Chain: A: PDB Molecule:fumarate reductase, flavoprotein subunit; PDBTitle: solution nmr structure of fumarate reductase flavoprotein subunit from2 lactobacillus plantarum, northeast structural genomics consortium3 target lpr145j 12 d2ofya1 16.2 11 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 13 d1siga_ 15.2 11 Fold:Sigma2 domain of RNA polymerase sigma factors Superfamily:Sigma2 domain of RNA polymerase sigma factors Family:Sigma2 domain of RNA polymerase sigma factors 14 c2a6eF_ 14.6 16 PDB header:transferase Chain: F: PDB Molecule:rna polymerase sigma factor rpod; PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme 15 d1smyf3 13.5 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 16 d1ku2a2 13.3 15 Fold:Sigma2 domain of RNA polymerase sigma factors Superfamily:Sigma2 domain of RNA polymerase sigma factors Family:Sigma2 domain of RNA polymerase sigma factors 17 d1iyjb3 13.0 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 18 d1hlva1 12.8 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 19 d2cx1a1 12.3 30 Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain 20 d1bxla_ 11.3 4 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 21 d1rr7a_ not modelled 11.2 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor 22 c1rr7A_ not modelled 11.2 17 PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu 23 c1ku2A_ not modelled 11.1 16 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 24 d1d4ca3 not modelled 10.6 32 Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 25 c2yv6A_ not modelled 10.4 4 PDB header:apoptosis Chain: A: PDB Molecule:bcl-2 homologous antagonist/killer; PDBTitle: crystal structure of human bcl-2 family protein bak 26 c1l9uH_ not modelled 10.3 16 PDB header:transcription Chain: H: PDB Molecule:sigma factor siga; PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution 27 d6paxa1 not modelled 10.2 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 28 c2w48D_ not modelled 10.1 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 29 d1miua3 not modelled 9.7 27 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 30 d1bw6a_ not modelled 9.6 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 31 c3d79A_ not modelled 9.3 13 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein ph0734; PDBTitle: crystal structure of hypothetical protein ph0734.1 from2 hyperthermophilic archaea pyrococcus horikoshii ot3 32 d1g5ma_ not modelled 8.9 4 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 33 d1o0la_ not modelled 8.7 4 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 34 c2o2fA_ not modelled 8.5 4 PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator bcl-2; PDBTitle: solution structure of the anti-apoptotic protein bcl-2 in2 complex with an acyl-sulfonamide-based ligand 35 c2gm4B_ not modelled 8.2 24 PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna 36 d1zy3a1 not modelled 8.2 4 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 37 d2bt6a1 not modelled 8.0 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin-related 38 c2x48B_ not modelled 7.8 21 PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 39 d2ponb1 not modelled 7.6 4 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 40 d2fug33 not modelled 7.4 11 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin domains from multidomain proteins 41 c3f56F_ not modelled 7.0 32 PDB header:structural protein Chain: F: PDB Molecule:csos1d; PDBTitle: the structure of a previously undetected carboxysome shell2 protein: csos1d from prochlorococcus marinus med4 42 c2xa0A_ not modelled 7.0 4 PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator bcl-2; PDBTitle: crystal structure of bcl-2 in complex with a bax bh32 peptide 43 c2vofA_ not modelled 7.0 4 PDB header:apoptosis Chain: A: PDB Molecule:bcl-2-related protein a1; PDBTitle: structure of mouse a1 bound to the puma bh3-domain 44 d1u9ka_ not modelled 6.6 31 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 45 c3t76A_ not modelled 6.6 26 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 46 c1y6uA_ not modelled 6.5 19 PDB header:dna binding protein Chain: A: PDB Molecule:excisionase from transposon tn916; PDBTitle: the structure of the excisionase (xis) protein from2 conjugative transposon tn916 provides insights into the3 regulation of heterobivalent tyrosine recombinases 47 d1ysga1 not modelled 6.1 4 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 48 c3b7hA_ not modelled 5.9 11 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 49 c1zs7A_ not modelled 5.9 30 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ape0525; PDBTitle: the structure of gene product ape0525 from aeropyrum pernix 50 c2rrdA_ not modelled 5.9 7 PDB header:dna binding protein Chain: A: PDB Molecule:hrdc domain from bloom syndrome protein; PDBTitle: structure of hrdc domain from human bloom syndrome protein, blm 51 c2kpjA_ not modelled 5.8 6 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 52 d1pq1a_ not modelled 5.7 4 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 53 c2rn7A_ not modelled 5.4 10 PDB header:unknown function Chain: A: PDB Molecule:is629 orfa; PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125 54 c2aukA_ not modelled 5.4 42 PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase beta' chain; PDBTitle: structure of e. coli rna polymerase beta' g/g' insert 55 d1jala2 not modelled 5.4 36 Fold:beta-Grasp (ubiquitin-like) Superfamily:TGS-like Family:G domain-linked domain 56 d1y9qa2 not modelled 5.3 14 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Probable transcriptional regulator VC1968, C-terminal domain 57 d1wi0a_ not modelled 5.3 28 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 58 d1p9ka_ not modelled 5.3 18 Fold:Alpha-L RNA-binding motif Superfamily:Alpha-L RNA-binding motif Family:YbcJ-like 59 c3clcC_ not modelled 5.2 25 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 60 c2yxyA_ not modelled 5.2 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical conserved protein, gk0453; PDBTitle: crystarl structure of hypothetical conserved protein, gk0453 61 c1u78A_ not modelled 5.1 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 62 c2ewtA_ not modelled 5.1 12 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd

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