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

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C

A

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L

W

K

K

I

I

A

L

Y

E

Q

A

A

E

C

D

G

E

V

V

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P

K

E

P

N

W

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A

W

A

N

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I

R

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M

C

V

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D

G

R

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H

K

Q

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C

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M

Y

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R

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

V

S

R

D

P

F

W

C

R

N

V

L

S

P

S

K

L

R

E

K

W

D

E

L

S

L

R

L

S

P

S

V

S

T

Y

T

E

K

R

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D

P

Y

F

K

A

S

Y

D

N

V

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Y

S

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I

P

A

G

F

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

R

G

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 3c9p chain A Region: 44 - 65 Aligned: 22 Modelled: 22 Confidence: 45.8% Identity: 9% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917 Phyre2 PDB 1a92 chain B Region: 33 - 71 Aligned: 38 Modelled: 39 Confidence: 40.9% Identity: 13% PDB header:leucine zipper Chain: B: PDB Molecule:delta antigen; PDBTitle: oligomerization domain of hepatitis delta antigen Phyre2 PDB 1k8i chain A domain 2 Region: 28 - 40 Aligned: 13 Modelled: 13 Confidence: 23.2% Identity: 31% Fold: MHC antigen-recognition domain Superfamily: MHC antigen-recognition domain Family: MHC antigen-recognition domain Phyre2 PDB 2bs2 chain A domain 1 Region: 107 - 122 Aligned: 16 Modelled: 16 Confidence: 13.4% Identity: 38% Fold: Spectrin repeat-like Superfamily: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain Family: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain Phyre2 PDB 2fug chain 6 domain 1 Region: 45 - 67 Aligned: 23 Modelled: 23 Confidence: 10.5% Identity: 9% Fold: HydA/Nqo6-like Superfamily: HydA/Nqo6-like Family: Nq06-like Phyre2 PDB 2jtv chain A Region: 37 - 46 Aligned: 10 Modelled: 10 Confidence: 10.4% Identity: 20% PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384 Phyre2 PDB 3izc chain H Region: 47 - 79 Aligned: 33 Modelled: 33 Confidence: 9.7% Identity: 12% PDB header:ribosome Chain: H: PDB Molecule:60s ribosomal protein rpl8 (l7ae); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 2vvy chain C Region: 4 - 63 Aligned: 50 Modelled: 60 Confidence: 9.4% Identity: 16% PDB header:viral protein Chain: C: PDB Molecule:protein b15; PDBTitle: structure of vaccinia virus protein b14 Phyre2 PDB 1hdm chain A domain 2 Region: 28 - 39 Aligned: 12 Modelled: 12 Confidence: 9.0% Identity: 42% Fold: MHC antigen-recognition domain Superfamily: MHC antigen-recognition domain Family: MHC antigen-recognition domain Phyre2 PDB 1xkm chain C Region: 114 - 120 Aligned: 7 Modelled: 7 Confidence: 8.8% Identity: 43% PDB header:antibiotic Chain: C: PDB Molecule:distinctin chain a; PDBTitle: nmr structure of antimicrobial peptide distinctin in water Phyre2 PDB 1xkm chain A Region: 114 - 120 Aligned: 7 Modelled: 7 Confidence: 8.7% Identity: 43% PDB header:antibiotic Chain: A: PDB Molecule:distinctin chain a; PDBTitle: nmr structure of antimicrobial peptide distinctin in water Phyre2 PDB 2bpb chain B Region: 27 - 64 Aligned: 38 Modelled: 38 Confidence: 7.8% Identity: 11% PDB header:oxidoreductase Chain: B: PDB Molecule:sulfite\:cytochrome c oxidoreductase subunit b; PDBTitle: sulfite dehydrogenase from starkeya novella Phyre2 PDB 2gli chain A domain 5 Region: 74 - 83 Aligned: 10 Modelled: 10 Confidence: 7.2% Identity: 40% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 2d35 chain A Region: 34 - 42 Aligned: 9 Modelled: 9 Confidence: 6.6% Identity: 56% PDB header:cell cycle Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure of cell division reactivation factor,2 ceda Phyre2 PDB 2bn8 chain A Region: 34 - 42 Aligned: 9 Modelled: 9 Confidence: 6.2% Identity: 56% PDB header:cell cycle protein Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure and interactions of the e.coli cell2 division activator protein ceda Phyre2 PDB 3e0z chain B Region: 52 - 71 Aligned: 20 Modelled: 20 Confidence: 5.9% Identity: 15% PDB header:unknown function Chain: B: PDB Molecule:protein of unknown function; PDBTitle: crystal structure of a putative imidazole glycerol phosphate synthase2 homolog (eubrec_1070) from eubacterium rectale at 1.75 a resolution Phyre2 PDB 1nsa chain A domain 2 Region: 49 - 89 Aligned: 41 Modelled: 41 Confidence: 5.6% Identity: 12% Fold: Ferredoxin-like Superfamily: Protease propeptides/inhibitors Family: Pancreatic carboxypeptidase, activation domain Phyre2 PDB 3rys chain A Region: 37 - 91 Aligned: 53 Modelled: 55 Confidence: 5.5% Identity: 8% PDB header:hydrolase Chain: A: PDB Molecule:adenosine deaminase 1; PDBTitle: the crystal structure of adenine deaminase (aaur1117) from2 arthrobacter aurescens Phyre2 PDB 2y92 chain A Region: 34 - 122 Aligned: 81 Modelled: 89 Confidence: 5.3% Identity: 11% PDB header:immune system Chain: A: PDB Molecule:toll/interleukin-1 receptor domain-containing adapter PDBTitle: crystal structure of mal adaptor protein Phyre2 PDB 3ngv chain A Region: 49 - 100 Aligned: 50 Modelled: 52 Confidence: 5.1% Identity: 14% PDB header:transport protein Chain: A: PDB Molecule:d7 protein; PDBTitle: crystal structure of anst-d7l1 Phyre2 1 c3c9pA_ 2 c1a92B_ 3 d1k8ia2 4 d2bs2a1 5 d2fug61 6 c2jtvA_ 7 c3izcH_ 8 c2vvyC_ 9 d1hdma2 10 c1xkmC_ 11 c1xkmA_ 12 c2bpbB_ 13 d2glia5 14 c2d35A_ 15 c2bn8A_ 16 c3e0zB_ 17 d1nsaa2 18 c3rysA_ 19 c2y92A_ 20 c3ngvA_

Detailed template information

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

1 c3c9pA_ 45.8 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917 2 c1a92B_ 40.9 13 PDB header:leucine zipper Chain: B: PDB Molecule:delta antigen; PDBTitle: oligomerization domain of hepatitis delta antigen 3 d1k8ia2 23.2 31 Fold:MHC antigen-recognition domain Superfamily:MHC antigen-recognition domain Family:MHC antigen-recognition domain 4 d2bs2a1 13.4 38 Fold:Spectrin repeat-like Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain 5 d2fug61 10.5 9 Fold:HydA/Nqo6-like Superfamily:HydA/Nqo6-like Family:Nq06-like 6 c2jtvA_ 10.4 20 PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384 7 c3izcH_ 9.7 12 PDB header:ribosome Chain: H: PDB Molecule:60s ribosomal protein rpl8 (l7ae); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 8 c2vvyC_ 9.4 16 PDB header:viral protein Chain: C: PDB Molecule:protein b15; PDBTitle: structure of vaccinia virus protein b14 9 d1hdma2 9.0 42 Fold:MHC antigen-recognition domain Superfamily:MHC antigen-recognition domain Family:MHC antigen-recognition domain 10 c1xkmC_ 8.8 43 PDB header:antibiotic Chain: C: PDB Molecule:distinctin chain a; PDBTitle: nmr structure of antimicrobial peptide distinctin in water 11 c1xkmA_ 8.7 43 PDB header:antibiotic Chain: A: PDB Molecule:distinctin chain a; PDBTitle: nmr structure of antimicrobial peptide distinctin in water 12 c2bpbB_ 7.8 11 PDB header:oxidoreductase Chain: B: PDB Molecule:sulfite\:cytochrome c oxidoreductase subunit b; PDBTitle: sulfite dehydrogenase from starkeya novella 13 d2glia5 7.2 40 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 14 c2d35A_ 6.6 56 PDB header:cell cycle Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure of cell division reactivation factor,2 ceda 15 c2bn8A_ 6.2 56 PDB header:cell cycle protein Chain: A: PDB Molecule:cell division activator ceda; PDBTitle: solution structure and interactions of the e.coli cell2 division activator protein ceda 16 c3e0zB_ 5.9 15 PDB header:unknown function Chain: B: PDB Molecule:protein of unknown function; PDBTitle: crystal structure of a putative imidazole glycerol phosphate synthase2 homolog (eubrec_1070) from eubacterium rectale at 1.75 a resolution 17 d1nsaa2 5.6 12 Fold:Ferredoxin-like Superfamily:Protease propeptides/inhibitors Family:Pancreatic carboxypeptidase, activation domain 18 c3rysA_ 5.5 8 PDB header:hydrolase Chain: A: PDB Molecule:adenosine deaminase 1; PDBTitle: the crystal structure of adenine deaminase (aaur1117) from2 arthrobacter aurescens 19 c2y92A_ 5.3 11 PDB header:immune system Chain: A: PDB Molecule:toll/interleukin-1 receptor domain-containing adapter PDBTitle: crystal structure of mal adaptor protein 20 c3ngvA_ 5.1 14 PDB header:transport protein Chain: A: PDB Molecule:d7 protein; PDBTitle: crystal structure of anst-d7l1

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