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

S

T

K

N

R

T

R

R

T

T

T

R

N

I

R

F

P

N

Q

M

I

E

Q

I

N

I

A

L

E

Q

K

G

S

G

N

F

S

A

W

V

I

E

A

C

R

R

R

L

C

S

E

K

R

V

S

S

E

A

N

Secondary structure

SS confidence

Disorder

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?

Disorder confidence

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70

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Sequence

K

E

K

S

D

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E

L

L

R

K

Q

V

R

P

D

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 2bj7 chain A domain 1 Region: 14 - 53 Aligned: 40 Modelled: 40 Confidence: 70.8% Identity: 20% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2hza chain B domain 1 Region: 14 - 52 Aligned: 39 Modelled: 39 Confidence: 63.3% Identity: 21% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2hza chain A domain 1 Region: 14 - 50 Aligned: 37 Modelled: 37 Confidence: 55.8% Identity: 19% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2ca9 chain B Region: 14 - 50 Aligned: 37 Modelled: 37 Confidence: 48.9% Identity: 14% 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 2bj3 chain D Region: 14 - 50 Aligned: 37 Modelled: 37 Confidence: 39.6% Identity: 22% PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo Phyre2 PDB 1q5v chain B Region: 14 - 53 Aligned: 40 Modelled: 40 Confidence: 33.3% Identity: 20% PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr Phyre2 PDB 1y9b chain A domain 1 Region: 14 - 49 Aligned: 36 Modelled: 36 Confidence: 25.3% Identity: 14% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: VCA0319-like Phyre2 PDB 2i5u chain A domain 1 Region: 21 - 54 Aligned: 34 Modelled: 32 Confidence: 24.0% Identity: 12% Fold: DnaD domain-like Superfamily: DnaD domain-like Family: DnaD domain Phyre2 PDB 1qu3 chain A domain 1 Region: 19 - 75 Aligned: 57 Modelled: 57 Confidence: 21.6% Identity: 12% Fold: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Phyre2 PDB 1wn4 chain A Region: 18 - 33 Aligned: 16 Modelled: 16 Confidence: 20.9% Identity: 38% PDB header:plant protein Chain: A: PDB Molecule:vontr protein; PDBTitle: nmr structure of vontr Phyre2 PDB 1ku2 chain A domain 1 Region: 15 - 28 Aligned: 14 Modelled: 14 Confidence: 17.9% Identity: 50% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma3 domain Phyre2 PDB 2lf0 chain A Region: 42 - 72 Aligned: 31 Modelled: 31 Confidence: 16.7% Identity: 13% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yibl; PDBTitle: solution structure of sf3636, a two-domain unknown function protein2 from shigella flexneri 2a, determined by joint refinement of nmr,3 residual dipolar couplings and small-angle x-ray scatting, nesg4 target sfr339/ocsp target sf3636 Phyre2 PDB 2c5r chain A domain 1 Region: 14 - 25 Aligned: 12 Modelled: 12 Confidence: 16.3% Identity: 50% Fold: Phage replication organizer domain Superfamily: Phage replication organizer domain Family: Phage replication organizer domain Phyre2 PDB 1mnt chain A Region: 14 - 35 Aligned: 22 Modelled: 22 Confidence: 15.8% Identity: 27% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Arc/Mnt-like phage repressors Phyre2 PDB 2k53 chain A Region: 18 - 33 Aligned: 16 Modelled: 16 Confidence: 14.4% Identity: 19% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:a3dk08 protein; PDBTitle: nmr solution structure of a3dk08 protein from clostridium2 thermocellum: northeast structural genomics consortium3 target cmr9 Phyre2 PDB 2aga chain A Region: 33 - 48 Aligned: 16 Modelled: 16 Confidence: 14.3% Identity: 38% PDB header:transcription Chain: A: PDB Molecule:machado-joseph disease protein 1; PDBTitle: de-ubiquitinating function of ataxin-3: insights from the2 solution structure of the josephin domain Phyre2 PDB 2y0f chain D Region: 15 - 48 Aligned: 33 Modelled: 34 Confidence: 10.7% Identity: 9% PDB header:oxidoreductase Chain: D: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; PDBTitle: structure of gcpe (ispg) from thermus thermophilus hb27 Phyre2 PDB 2l3y chain A Region: 5 - 51 Aligned: 37 Modelled: 47 Confidence: 9.9% Identity: 27% PDB header:transcription Chain: A: PDB Molecule:interleukin-6; PDBTitle: solution structure of mouse il-6 Phyre2 PDB 1m56 chain D Region: 31 - 45 Aligned: 15 Modelled: 15 Confidence: 8.6% Identity: 27% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1yzm chain A domain 1 Region: 18 - 28 Aligned: 11 Modelled: 11 Confidence: 8.4% Identity: 18% Fold: Long alpha-hairpin Superfamily: Rabenosyn-5 Rab-binding domain-like Family: Rabenosyn-5 Rab-binding domain-like Phyre2 1 d2bj7a1 2 d2hzab1 3 d2hzaa1 4 c2ca9B_ 5 c2bj3D_ 6 c1q5vB_ 7 d1y9ba1 8 d2i5ua1 9 d1qu3a1 10 c1wn4A_ 11 d1ku2a1 12 c2lf0A_ 13 d2c5ra1 14 d1mnta_ 15 c2k53A_ 16 c2agaA_ 17 c2y0fD_ 18 c2l3yA_ 19 d1m56d_ 20 d1yzma1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 d2bj7a1 70.8 20 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 2 d2hzab1 63.3 21 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 3 d2hzaa1 55.8 19 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 4 c2ca9B_ 48.9 14 PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation 5 c2bj3D_ 39.6 22 PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo 6 c1q5vB_ 33.3 20 PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr 7 d1y9ba1 25.3 14 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VCA0319-like 8 d2i5ua1 24.0 12 Fold:DnaD domain-like Superfamily:DnaD domain-like Family:DnaD domain 9 d1qu3a1 21.6 12 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 10 c1wn4A_ 20.9 38 PDB header:plant protein Chain: A: PDB Molecule:vontr protein; PDBTitle: nmr structure of vontr 11 d1ku2a1 17.9 50 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 12 c2lf0A_ 16.7 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yibl; PDBTitle: solution structure of sf3636, a two-domain unknown function protein2 from shigella flexneri 2a, determined by joint refinement of nmr,3 residual dipolar couplings and small-angle x-ray scatting, nesg4 target sfr339/ocsp target sf3636 13 d2c5ra1 16.3 50 Fold:Phage replication organizer domain Superfamily:Phage replication organizer domain Family:Phage replication organizer domain 14 d1mnta_ 15.8 27 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 15 c2k53A_ 14.4 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:a3dk08 protein; PDBTitle: nmr solution structure of a3dk08 protein from clostridium2 thermocellum: northeast structural genomics consortium3 target cmr9 16 c2agaA_ 14.3 38 PDB header:transcription Chain: A: PDB Molecule:machado-joseph disease protein 1; PDBTitle: de-ubiquitinating function of ataxin-3: insights from the2 solution structure of the josephin domain 17 c2y0fD_ 10.7 9 PDB header:oxidoreductase Chain: D: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; PDBTitle: structure of gcpe (ispg) from thermus thermophilus hb27 18 c2l3yA_ 9.9 27 PDB header:transcription Chain: A: PDB Molecule:interleukin-6; PDBTitle: solution structure of mouse il-6 19 d1m56d_ 8.6 27 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 20 d1yzma1 8.4 18 Fold:Long alpha-hairpin Superfamily:Rabenosyn-5 Rab-binding domain-like Family:Rabenosyn-5 Rab-binding domain-like 21 d1pd3a_ not modelled 8.1 60 Fold:ROP-like Superfamily:Nonstructural protein ns2, Nep, M1-binding domain Family:Nonstructural protein ns2, Nep, M1-binding domain 22 c2p22D_ not modelled 8.1 22 PDB header:transport protein Chain: D: PDB Molecule:hypothetical 12.0 kda protein in ade3-ser2 PDBTitle: structure of the yeast escrt-i heterotetramer core 23 d1i1rb_ not modelled 7.8 58 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Long-chain cytokines 24 d1mg7a2 not modelled 7.4 25 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Early switch protein XOL-1 25 d1kkea1 not modelled 7.2 41 Fold:Triple beta-spiral Superfamily:Fibre shaft of virus attachment proteins Family:Reovirus attachment protein sigma 1 26 d1ivsa2 not modelled 7.1 21 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 27 d1z0kb1 not modelled 6.6 25 Fold:Long alpha-hairpin Superfamily:Rabenosyn-5 Rab-binding domain-like Family:Rabenosyn-5 Rab-binding domain-like 28 d3saka_ not modelled 6.4 43 Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain 29 d1mvfd_ not modelled 6.4 23 Fold:Double-split beta-barrel Superfamily:AbrB/MazE/MraZ-like Family:Kis/PemI addiction antidote 30 d1az3a_ not modelled 6.0 42 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease EcoRV 31 d1vq3a_ not modelled 5.8 33 Fold:PurS-like Superfamily:PurS-like Family:PurS subunit of FGAM synthetase 32 d1ffya1 not modelled 5.7 12 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 33 c3kz5E_ not modelled 5.7 43 PDB header:dna binding protein Chain: E: PDB Molecule:protein sopb; PDBTitle: structure of cdomain 34 d1gs0a1 not modelled 5.5 20 Fold:Domain of poly(ADP-ribose) polymerase Superfamily:Domain of poly(ADP-ribose) polymerase Family:Domain of poly(ADP-ribose) polymerase 35 c1u9pA_ not modelled 5.3 13 PDB header:unknown function Chain: A: PDB Molecule:parc; PDBTitle: permuted single-chain arc 36 c3ostA_ not modelled 5.2 27 PDB header:lipid binding protein Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4; PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p

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