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

G

I

L

T

R

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R

Q

F

G

K

R

Y

F

W

P

H

L

L

L

G

M

V

A

A

S

L

G

L

P

A

L

S

N

A

A

E

P

N

A

P

A

K

A

T

T

R

N

H

E

P

S

A

K

V

N

F

G

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

Q

L

A

L

L

E

A

N

T

R

R

P

N

S

N

Y

S

V

D

Y

W

H

Q

H

A

I

R

T

V

I

R

H

L

S

F

A

M

A

P

Q

T

L

P

V

A

E

E

S

L

P

L

Q

A

Q

H

L

A

L

L

D

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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150

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160

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170

Sequence

T

L

S

A

L

L

T

Q

E

G

T

P

S

E

K

G

Y

R

I

D

Y

A

H

F

T

P

Q

A

K

F

S

T

P

V

W

I

S

Q

A

Q

G

I

R

A

G

P

Q

R

L

T

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 3ibp chain A Region: 82 - 114 Aligned: 33 Modelled: 33 Confidence: 24.8% Identity: 18% PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: the crystal structure of the dimerization domain of escherichia coli2 structural maintenance of chromosomes protein mukb Phyre2 PDB 3ost chain A Region: 4 - 12 Aligned: 9 Modelled: 9 Confidence: 20.8% Identity: 44% PDB header:lipid binding protein Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4; PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p Phyre2 PDB 1wdk chain A domain 2 Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 12.8% Identity: 15% Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like Family: HCDH C-domain-like Phyre2 PDB 1jb0 chain X Region: 14 - 24 Aligned: 11 Modelled: 11 Confidence: 12.4% Identity: 55% PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i subunit psax; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria Phyre2 PDB 1jb0 chain X Region: 14 - 24 Aligned: 11 Modelled: 11 Confidence: 12.4% Identity: 55% Fold: Single transmembrane helix Superfamily: Subunit PsaX of photosystem I reaction centre Family: Subunit PsaX of photosystem I reaction centre Phyre2 PDB 3pcq chain X Region: 14 - 24 Aligned: 11 Modelled: 11 Confidence: 11.6% Identity: 55% PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i 4.8k protein; PDBTitle: femtosecond x-ray protein nanocrystallography Phyre2 PDB 1zmb chain A domain 1 Region: 9 - 17 Aligned: 9 Modelled: 9 Confidence: 11.0% Identity: 67% Fold: Flavodoxin-like Superfamily: SGNH hydrolase Family: Putative acetylxylan esterase-like Phyre2 PDB 1yle chain A domain 1 Region: 1 - 16 Aligned: 16 Modelled: 16 Confidence: 10.3% Identity: 25% Fold: Acyl-CoA N-acyltransferases (Nat) Superfamily: Acyl-CoA N-acyltransferases (Nat) Family: AstA-like Phyre2 PDB 2ks1 chain B Region: 20 - 31 Aligned: 12 Modelled: 12 Confidence: 9.5% Identity: 58% PDB header:transferase Chain: B: PDB Molecule:epidermal growth factor receptor; PDBTitle: heterodimeric association of transmembrane domains of erbb1 and erbb22 receptors enabling kinase activation Phyre2 PDB 2fiq chain A domain 1 Region: 12 - 19 Aligned: 8 Modelled: 8 Confidence: 9.4% Identity: 63% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: GatZ-like Phyre2 PDB 2izv chain A domain 1 Region: 83 - 94 Aligned: 12 Modelled: 12 Confidence: 9.2% Identity: 50% Fold: SOCS box-like Superfamily: SOCS box-like Family: SOCS box-like Phyre2 PDB 3nnq chain A Region: 3 - 20 Aligned: 18 Modelled: 12 Confidence: 8.2% Identity: 6% PDB header:viral protein Chain: A: PDB Molecule:n-terminal domain of moloney murine leukemia virus PDBTitle: crystal structure of the n-terminal domain of moloney murine leukemia2 virus integrase, northeast structural genomics consortium target or3 Phyre2 PDB 1hly chain A Region: 161 - 165 Aligned: 5 Modelled: 5 Confidence: 7.9% Identity: 100% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 1g3n chain C domain 2 Region: 75 - 90 Aligned: 15 Modelled: 16 Confidence: 7.8% Identity: 40% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 1vf5 chain G Region: 20 - 30 Aligned: 11 Modelled: 11 Confidence: 7.0% Identity: 64% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1vf5 chain G Region: 20 - 30 Aligned: 11 Modelled: 11 Confidence: 7.0% Identity: 64% PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2e74 chain G domain 1 Region: 20 - 30 Aligned: 11 Modelled: 11 Confidence: 6.9% Identity: 64% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 2e76 chain D Region: 11 - 30 Aligned: 20 Modelled: 20 Confidence: 6.7% Identity: 30% PDB header:photosynthesis Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus Phyre2 PDB 2qdo chain C Region: 88 - 93 Aligned: 6 Modelled: 6 Confidence: 6.5% Identity: 67% PDB header:photosynthesis Chain: C: PDB Molecule:nbla protein; PDBTitle: nbla protein from t. vulcanus Phyre2 PDB 3d7v chain B Region: 151 - 158 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 38% PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: crystal structure of mcl-1 in complex with an mcl-12 selective bh3 ligand Phyre2 1 c3ibpA_ 2 c3ostA_ 3 d1wdka2 4 c1jb0X_ 5 d1jb0x_ 6 c3pcqX_ 7 d1zmba1 8 d1ylea1 9 c2ks1B_ 10 d2fiqa1 11 d2izva1 12 c3nnqA_ 13 d1hlya_ 14 d1g3nc2 15 d1vf5g_ 16 c1vf5G_ 17 d2e74g1 18 c2e76D_ 19 c2qdoC_ 20 c3d7vB_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 c3ibpA_ 24.8 18 PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: the crystal structure of the dimerization domain of escherichia coli2 structural maintenance of chromosomes protein mukb 2 c3ostA_ 20.8 44 PDB header:lipid binding protein Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4; PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p 3 d1wdka2 12.8 15 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:HCDH C-domain-like 4 c1jb0X_ 12.4 55 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i subunit psax; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 5 d1jb0x_ 12.4 55 Fold:Single transmembrane helix Superfamily:Subunit PsaX of photosystem I reaction centre Family:Subunit PsaX of photosystem I reaction centre 6 c3pcqX_ 11.6 55 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i 4.8k protein; PDBTitle: femtosecond x-ray protein nanocrystallography 7 d1zmba1 11.0 67 Fold:Flavodoxin-like Superfamily:SGNH hydrolase Family:Putative acetylxylan esterase-like 8 d1ylea1 10.3 25 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:AstA-like 9 c2ks1B_ 9.5 58 PDB header:transferase Chain: B: PDB Molecule:epidermal growth factor receptor; PDBTitle: heterodimeric association of transmembrane domains of erbb1 and erbb22 receptors enabling kinase activation 10 d2fiqa1 9.4 63 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:GatZ-like 11 d2izva1 9.2 50 Fold:SOCS box-like Superfamily:SOCS box-like Family:SOCS box-like 12 c3nnqA_ 8.2 6 PDB header:viral protein Chain: A: PDB Molecule:n-terminal domain of moloney murine leukemia virus PDBTitle: crystal structure of the n-terminal domain of moloney murine leukemia2 virus integrase, northeast structural genomics consortium target or3 13 d1hlya_ 7.9 100 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 14 d1g3nc2 7.8 40 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 15 d1vf5g_ 7.0 64 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 16 c1vf5G_ 7.0 64 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 17 d2e74g1 6.9 64 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 18 c2e76D_ 6.7 30 PDB header:photosynthesis Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus 19 c2qdoC_ 6.5 67 PDB header:photosynthesis Chain: C: PDB Molecule:nbla protein; PDBTitle: nbla protein from t. vulcanus 20 c3d7vB_ 6.2 38 PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: crystal structure of mcl-1 in complex with an mcl-12 selective bh3 ligand 21 c2kfdA_ not modelled 6.1 50 PDB header:nuclear protein Chain: A: PDB Molecule:pre-mrna-processing protein prp40; PDBTitle: prp40 ff4 domain 22 c1bm4A_ not modelled 6.0 40 PDB header:viral protein Chain: A: PDB Molecule:protein (moloney murine leukemia virus capsid); PDBTitle: momlv capsid protein major homology region peptide analog 23 c2vy8A_ not modelled 6.0 43 PDB header:transcription Chain: A: PDB Molecule:polymerase basic protein 2; PDBTitle: the 627-domain from influenza a virus polymerase pb22 subunit with glu-627 24 c3io9B_ not modelled 6.0 38 PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: biml12y in complex with mcl-1 25 c3kj2B_ not modelled 6.0 38 PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: mcl-1 in complex with bim bh3 mutant f4ae 26 c2nl9B_ not modelled 5.9 38 PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: crystal structure of the mcl-1:bim bh3 complex 27 d2nysa1 not modelled 5.9 54 Fold:SspB-like Superfamily:SspB-like Family:AGR C 3712p-like 28 c2nysA_ not modelled 5.9 54 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:agr_c_3712p; PDBTitle: x-ray crystal structure of protein agr_c_3712 from2 agrobacterium tumefaciens. northeast structural genomics3 consortium target atr88. 29 c3rfrI_ not modelled 5.6 35 PDB header:oxidoreductase Chain: I: PDB Molecule:pmob; PDBTitle: crystal structure of particulate methane monooxygenase (pmmo) from2 methylocystis sp. strain m 30 c2qazC_ not modelled 5.3 31 PDB header:hydrolase activator Chain: C: PDB Molecule:sspb protein; PDBTitle: structure of c. crescentus sspb ortholog 31 d2e74b1 not modelled 5.1 36 Fold:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

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