Secondary structure and disorder prediction

1

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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

V

T

N

L

Y

Q

N

M

R

A

N

A

L

A

D

A

E

L

R

R

K

A

A

D

E

L

T

C

M

T

A

R

I

N

R

G

E

T

I

P

E

P

V

K

Q

L

P

V

M

G

G

R

P

L

N

R

A

Q

A

Secondary structure

SS confidence

Disorder

?

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?

?

?

?

?

?

?

?

?

?

?

?

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?

?

?

?

?

?

?

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?

?

Disorder confidence

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70

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Sequence

L

A

K

I

A

E

I

K

A

K

F

G

L

K

G

A

S

V

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

Rank Aligned region

PDB 1c52 chain A Region: 13 - 74 Aligned: 58 Modelled: 62 Confidence: 69.9% Identity: 24% Fold: Cytochrome c Superfamily: Cytochrome c Family: monodomain cytochrome c Phyre2 PDB 3nuf chain B Region: 1 - 42 Aligned: 42 Modelled: 42 Confidence: 58.9% Identity: 19% PDB header:transcription regulator Chain: B: PDB Molecule:prd-containing transcription regulator; PDBTitle: crystal structure of a prd-containing transcription regulator2 (lsei_2718) from lactobacillus casei atcc 334 at 1.38 a resolution Phyre2 PDB 2yum chain A Region: 15 - 43 Aligned: 26 Modelled: 26 Confidence: 35.1% Identity: 8% PDB header:transcription Chain: A: PDB Molecule:zinc finger zz-type-containing protein 3; PDBTitle: solution structure of the myb-like dna-binding domain of2 human zzz3 protein Phyre2 PDB 1vz0 chain A domain 1 Region: 6 - 64 Aligned: 58 Modelled: 59 Confidence: 30.3% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: KorB DNA-binding domain-like Family: KorB DNA-binding domain-like Phyre2 PDB 2es9 chain A domain 1 Region: 4 - 40 Aligned: 32 Modelled: 32 Confidence: 25.3% Identity: 9% Fold: YoaC-like Superfamily: YoaC-like Family: YoaC-like Phyre2 PDB 2cjj chain A Region: 15 - 41 Aligned: 25 Modelled: 27 Confidence: 25.3% Identity: 20% PDB header:dna-binding protein Chain: A: PDB Molecule:radialis; PDBTitle: crystal structure of the myb domain of the rad2 transcription factor from antirrhinum majus Phyre2 PDB 2cjj chain A domain 1 Region: 15 - 41 Aligned: 25 Modelled: 27 Confidence: 25.3% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 1m98 chain A domain 1 Region: 29 - 43 Aligned: 15 Modelled: 15 Confidence: 18.6% Identity: 20% Fold: Orange carotenoid protein, N-terminal domain Superfamily: Orange carotenoid protein, N-terminal domain Family: Orange carotenoid protein, N-terminal domain Phyre2 PDB 1h99 chain A domain 1 Region: 2 - 74 Aligned: 71 Modelled: 73 Confidence: 17.2% Identity: 14% Fold: PTS-regulatory domain, PRD Superfamily: PTS-regulatory domain, PRD Family: PTS-regulatory domain, PRD Phyre2 PDB 2l66 chain B Region: 65 - 74 Aligned: 10 Modelled: 10 Confidence: 15.5% Identity: 40% PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, abrb family; PDBTitle: the dna-recognition fold of sso7c4 suggests a new member of spovt-abrb2 superfamily from archaea. Phyre2 PDB 3nzl chain A Region: 12 - 30 Aligned: 19 Modelled: 18 Confidence: 14.0% Identity: 16% PDB header:transcription Chain: A: PDB Molecule:dna-binding protein satb1; PDBTitle: crystal structure of the n-terminal domain of dna-binding protein2 satb1 from homo sapiens, northeast structural genomics consortium3 target hr4435b Phyre2 PDB 1zx4 chain B Region: 6 - 66 Aligned: 60 Modelled: 59 Confidence: 13.8% Identity: 13% PDB header:translation Chain: B: PDB Molecule:plasmid partition par b protein; PDBTitle: structure of parb bound to dna Phyre2 PDB 1m98 chain A Region: 29 - 43 Aligned: 15 Modelled: 15 Confidence: 12.9% Identity: 20% PDB header:unknown function Chain: A: PDB Molecule:orange carotenoid protein; PDBTitle: crystal structure of orange carotenoid protein Phyre2 PDB 1h99 chain A domain 2 Region: 1 - 74 Aligned: 74 Modelled: 74 Confidence: 11.4% Identity: 8% Fold: PTS-regulatory domain, PRD Superfamily: PTS-regulatory domain, PRD Family: PTS-regulatory domain, PRD Phyre2 PDB 1up8 chain A Region: 17 - 66 Aligned: 47 Modelled: 50 Confidence: 11.0% Identity: 23% Fold: Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily: Acid phosphatase/Vanadium-dependent haloperoxidase Family: Haloperoxidase (bromoperoxidase) Phyre2 PDB 2dsy chain A domain 1 Region: 15 - 41 Aligned: 27 Modelled: 27 Confidence: 10.7% Identity: 26% Fold: TTHA1013/TTHA0281-like Superfamily: TTHA1013/TTHA0281-like Family: TTHA0281-like Phyre2 PDB 2b7m chain A domain 1 Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 10.2% Identity: 17% Fold: alpha-alpha superhelix Superfamily: Cullin repeat-like Family: Exocyst complex component Phyre2 PDB 3gwh chain B Region: 27 - 74 Aligned: 48 Modelled: 48 Confidence: 9.5% Identity: 21% PDB header:transcription Chain: B: PDB Molecule:transcriptional antiterminator (bglg family); PDBTitle: crystallographic ab initio protein solution far below atomic2 resolution Phyre2 PDB 1hwx chain A domain 2 Region: 12 - 43 Aligned: 32 Modelled: 32 Confidence: 9.2% Identity: 19% Fold: Aminoacid dehydrogenase-like, N-terminal domain Superfamily: Aminoacid dehydrogenase-like, N-terminal domain Family: Aminoacid dehydrogenases Phyre2 PDB 2wj8 chain N Region: 17 - 50 Aligned: 32 Modelled: 34 Confidence: 8.8% Identity: 19% PDB header:rna binding protein/rna Chain: N: PDB Molecule:nucleoprotein; PDBTitle: respiratory syncitial virus ribonucleoprotein Phyre2 1 d1c52a_ 2 c3nufB_ 3 c2yumA_ 4 d1vz0a1 5 d2es9a1 6 c2cjjA_ 7 d2cjja1 8 d1m98a1 9 d1h99a1 10 c2l66B_ 11 c3nzlA_ 12 c1zx4B_ 13 c1m98A_ 14 d1h99a2 15 d1up8a_ 16 d2dsya1 17 d2b7ma1 18 c3gwhB_ 19 d1hwxa2 20 c2wj8N_ 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

Detailed template information

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

1 d1c52a_ 69.9 24 Fold:Cytochrome c Superfamily:Cytochrome c Family:monodomain cytochrome c 2 c3nufB_ 58.9 19 PDB header:transcription regulator Chain: B: PDB Molecule:prd-containing transcription regulator; PDBTitle: crystal structure of a prd-containing transcription regulator2 (lsei_2718) from lactobacillus casei atcc 334 at 1.38 a resolution 3 c2yumA_ 35.1 8 PDB header:transcription Chain: A: PDB Molecule:zinc finger zz-type-containing protein 3; PDBTitle: solution structure of the myb-like dna-binding domain of2 human zzz3 protein 4 d1vz0a1 30.3 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 5 d2es9a1 25.3 9 Fold:YoaC-like Superfamily:YoaC-like Family:YoaC-like 6 c2cjjA_ 25.3 20 PDB header:dna-binding protein Chain: A: PDB Molecule:radialis; PDBTitle: crystal structure of the myb domain of the rad2 transcription factor from antirrhinum majus 7 d2cjja1 25.3 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 8 d1m98a1 18.6 20 Fold:Orange carotenoid protein, N-terminal domain Superfamily:Orange carotenoid protein, N-terminal domain Family:Orange carotenoid protein, N-terminal domain 9 d1h99a1 17.2 14 Fold:PTS-regulatory domain, PRD Superfamily:PTS-regulatory domain, PRD Family:PTS-regulatory domain, PRD 10 c2l66B_ 15.5 40 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, abrb family; PDBTitle: the dna-recognition fold of sso7c4 suggests a new member of spovt-abrb2 superfamily from archaea. 11 c3nzlA_ 14.0 16 PDB header:transcription Chain: A: PDB Molecule:dna-binding protein satb1; PDBTitle: crystal structure of the n-terminal domain of dna-binding protein2 satb1 from homo sapiens, northeast structural genomics consortium3 target hr4435b 12 c1zx4B_ 13.8 13 PDB header:translation Chain: B: PDB Molecule:plasmid partition par b protein; PDBTitle: structure of parb bound to dna 13 c1m98A_ 12.9 20 PDB header:unknown function Chain: A: PDB Molecule:orange carotenoid protein; PDBTitle: crystal structure of orange carotenoid protein 14 d1h99a2 11.4 8 Fold:PTS-regulatory domain, PRD Superfamily:PTS-regulatory domain, PRD Family:PTS-regulatory domain, PRD 15 d1up8a_ 11.0 23 Fold:Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily:Acid phosphatase/Vanadium-dependent haloperoxidase Family:Haloperoxidase (bromoperoxidase) 16 d2dsya1 10.7 26 Fold:TTHA1013/TTHA0281-like Superfamily:TTHA1013/TTHA0281-like Family:TTHA0281-like 17 d2b7ma1 10.2 17 Fold:alpha-alpha superhelix Superfamily:Cullin repeat-like Family:Exocyst complex component 18 c3gwhB_ 9.5 21 PDB header:transcription Chain: B: PDB Molecule:transcriptional antiterminator (bglg family); PDBTitle: crystallographic ab initio protein solution far below atomic2 resolution 19 d1hwxa2 9.2 19 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 20 c2wj8N_ 8.8 19 PDB header:rna binding protein/rna Chain: N: PDB Molecule:nucleoprotein; PDBTitle: respiratory syncitial virus ribonucleoprotein 21 d1ufza_ not modelled 8.8 15 Fold:RuvA C-terminal domain-like Superfamily:HBS1-like domain Family:HBS1-like domain 22 d1ddba_ not modelled 8.7 19 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 23 d2gmya1 not modelled 8.7 23 Fold:AhpD-like Superfamily:AhpD-like Family:Atu0492-like 24 d1b5qa2 not modelled 8.0 18 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:L-aminoacid/polyamine oxidase 25 c2wvmA_ not modelled 7.8 32 PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: h309a mutant of mannosyl-3-phosphoglycerate synthase from2 thermus thermophilus hb27 in complex with3 gdp-alpha-d-mannose and mg(ii) 26 d1toha_ not modelled 7.6 21 Fold:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Superfamily:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Family:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains 27 c3gocB_ not modelled 7.5 21 PDB header:hydrolase Chain: B: PDB Molecule:endonuclease v; PDBTitle: crystal structure of the endonuclease v (sav1684) from streptomyces2 avermitilis. northeast structural genomics consortium target svr196 28 c2zu8A_ not modelled 7.2 23 PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: crystal structure of mannosyl-3-phosphoglycerate synthase2 from pyrococcus horikoshii 29 d2v5za2 not modelled 7.2 18 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:L-aminoacid/polyamine oxidase 30 d1j8ua_ not modelled 7.1 18 Fold:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Superfamily:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Family:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains 31 d1phza2 not modelled 6.9 18 Fold:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Superfamily:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Family:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains 32 d1l1fa2 not modelled 6.8 22 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 33 d2fhzb1 not modelled 6.7 5 Fold:Colicin D/E5 nuclease domain Superfamily:Colicin D/E5 nuclease domain Family:Colicin E5 nuclease domain 34 d1mlwa_ not modelled 6.6 18 Fold:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Superfamily:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains Family:Aromatic aminoacid monoxygenases, catalytic and oligomerization domains 35 d1ppjb2 not modelled 6.6 11 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:MPP-like 36 d1dgsa2 not modelled 6.4 50 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA ligase/mRNA capping enzyme postcatalytic domain 37 c1uixA_ not modelled 6.4 67 PDB header:transferase Chain: A: PDB Molecule:rho-associated kinase; PDBTitle: coiled-coil structure of the rhoa-binding domain in rho-2 kinase 38 c3bboW_ not modelled 6.4 33 PDB header:ribosome Chain: W: PDB Molecule:ribosomal protein l24; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 39 d1szaa_ not modelled 6.3 13 Fold:alpha-alpha superhelix Superfamily:ENTH/VHS domain Family:RPR domain (SMART 00582 ) 40 d1tjla2 not modelled 6.2 16 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Prokaryotic DksA/TraR C4-type zinc finger 41 c3jroA_ not modelled 6.1 20 PDB header:transport protein, structural protein Chain: A: PDB Molecule:fusion protein of protein transport protein sec13 PDBTitle: nup84-nup145c-sec13 edge element of the npc lattice 42 c1s1cY_ not modelled 6.1 67 PDB header:signaling protein Chain: Y: PDB Molecule:rho-associated, coiled-coil containing protein PDBTitle: crystal structure of the complex between the human rhoa and2 rho-binding domain of human rocki 43 c2d3jA_ not modelled 6.0 19 PDB header:signaling protein inhibitor Chain: A: PDB Molecule:wnt inhibitory factor-1; PDBTitle: nmr structure of the wif domain from human wif-1 44 c2vo4A_ not modelled 5.9 13 PDB header:transferase Chain: A: PDB Molecule:2,4-d inducible glutathione s-transferase; PDBTitle: glutathione transferase from glycine max 45 c2phmA_ not modelled 5.8 18 PDB header:oxidoreductase Chain: A: PDB Molecule:protein (phenylalanine-4-hydroxylase); PDBTitle: structure of phenylalanine hydroxylase dephosphorylated 46 d2fzva1 not modelled 5.7 17 Fold:Flavodoxin-like Superfamily:Flavoproteins Family:NADPH-dependent FMN reductase 47 d1b8za_ not modelled 5.6 13 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 48 c3hahA_ not modelled 5.5 18 PDB header:endocytosis Chain: A: PDB Molecule:human pacsin1 f-bar; PDBTitle: crystal structure of human pacsin1 f-bar domain (c2 lattice) 49 c3bg1F_ not modelled 5.4 20 PDB header:protein transport, hydrolase Chain: F: PDB Molecule:nucleoporin nup145; PDBTitle: architecture of a coat for the nuclear pore membrane 50 c2p1iA_ not modelled 5.3 25 PDB header:oxidoreductase Chain: A: PDB Molecule:ribonucleotide reductase, small chain; PDBTitle: plasmodium yoelii ribonucleotide reductase subunit r2 (py03671) 51 d1bgva2 not modelled 5.3 22 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 52 d1oyja1 not modelled 5.3 15 Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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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