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

R

A

L

P

I

C

L

V

A

L

M

L

S

G

C

S

M

L

S

R

S

P

V

E

P

V

Q

S

T

A

P

Q

P

K

A

E

P

A

K

P

K

A

P

R

A

T

P

V

R

I

Y

T

N

A

E

E

L

V

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

K

P

F

R

D

L

G

E

V

S

G

D

S

C

Q

A

S

N

Q

D

S

P

P

S

I

P

T

A

R

K

R

M

Q

I

N

A

S

K

M

K

A

N

A

V

L

L

H

S

C

E

V

T

S

G

T

P

G

C

Y

R

Secondary structure

SS confidence

Disorder

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Disorder confidence

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130

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Sequence

Q

A

V

C

I

G

S

A

L

N

I

T

A

K

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 2y1b chain A Region: 47 - 132 Aligned: 86 Modelled: 86 Confidence: 100.0% Identity: 100% PDB header:membrane protein Chain: A: PDB Molecule:putative outer membrane protein, signal; PDBTitle: crystal structure of the e. coli outer membrane lipoprotein2 rcsf Phyre2 PDB 1vr4 chain A domain 1 Region: 51 - 131 Aligned: 80 Modelled: 81 Confidence: 97.1% Identity: 24% Fold: Dodecin subunit-like Superfamily: YbjQ-like Family: YbjQ-like Phyre2 PDB 3qkb chain B Region: 59 - 131 Aligned: 73 Modelled: 73 Confidence: 96.8% Identity: 10% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution Phyre2 PDB 1y2i chain C Region: 51 - 131 Aligned: 81 Modelled: 81 Confidence: 96.4% Identity: 16% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein s0862; PDBTitle: crystal structure of mcsg target apc27401 from shigella2 flexneri Phyre2 PDB 1y2i chain A Region: 51 - 131 Aligned: 81 Modelled: 81 Confidence: 96.3% Identity: 16% Fold: Dodecin subunit-like Superfamily: YbjQ-like Family: YbjQ-like Phyre2 PDB 2jz7 chain A Region: 51 - 105 Aligned: 46 Modelled: 55 Confidence: 42.6% Identity: 22% PDB header:selenium-binding protein Chain: A: PDB Molecule:selenium binding protein; PDBTitle: solution nmr structure of selenium-binding protein from2 methanococcus vannielii Phyre2 PDB 2gk3 chain A domain 1 Region: 53 - 106 Aligned: 53 Modelled: 53 Confidence: 16.7% Identity: 11% Fold: Flavodoxin-like Superfamily: Class I glutamine amidotransferase-like Family: STM3548-like Phyre2 PDB 2jna chain A domain 1 Region: 54 - 108 Aligned: 51 Modelled: 55 Confidence: 16.6% Identity: 10% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2kxh chain B Region: 86 - 103 Aligned: 18 Modelled: 18 Confidence: 12.0% Identity: 28% PDB header:protein binding Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1; PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide Phyre2 PDB 1n1i chain A domain 1 Region: 107 - 122 Aligned: 16 Modelled: 16 Confidence: 11.4% Identity: 38% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: EGF/Laminin Family: Merozoite surface protein 1 (MSP-1) Phyre2 PDB 1ob1 chain C domain 1 Region: 107 - 122 Aligned: 16 Modelled: 16 Confidence: 10.6% Identity: 31% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: EGF/Laminin Family: Merozoite surface protein 1 (MSP-1) Phyre2 PDB 1b9w chain A domain 1 Region: 107 - 122 Aligned: 16 Modelled: 16 Confidence: 10.4% Identity: 38% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: EGF/Laminin Family: Merozoite surface protein 1 (MSP-1) Phyre2 PDB 2cr9 chain A domain 1 Region: 27 - 103 Aligned: 67 Modelled: 68 Confidence: 7.9% Identity: 19% Fold: WGR domain-like Superfamily: WGR domain-like Family: WGR domain Phyre2 PDB 1eyf chain A Region: 42 - 64 Aligned: 23 Modelled: 23 Confidence: 7.3% Identity: 30% Fold: Ada DNA repair protein, N-terminal domain (N-Ada 10) Superfamily: Ada DNA repair protein, N-terminal domain (N-Ada 10) Family: Ada DNA repair protein, N-terminal domain (N-Ada 10) Phyre2 PDB 2stb chain I Region: 105 - 124 Aligned: 17 Modelled: 17 Confidence: 6.9% Identity: 24% PDB header:hydrolase/hydrolase inhibitor Chain: I: PDB Molecule:protein (trypsin inhibitor); PDBTitle: anionic salmon trypsin in complex with squash seed2 inhibitor (cucurbita pepo trypsin inhibitor ii) Phyre2 PDB 2sta chain I Region: 105 - 124 Aligned: 17 Modelled: 17 Confidence: 6.3% Identity: 29% PDB header:hydrolase/hydrolase inhibitor Chain: I: PDB Molecule:protein (trypsin inhibitor); PDBTitle: anionic salmon trypsin in complex with squash seed2 inhibitor (cucurbita maxima trypsin inhibitor i) Phyre2 PDB 2btc chain I Region: 105 - 124 Aligned: 17 Modelled: 17 Confidence: 6.1% Identity: 24% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Plant inhibitors of proteinases and amylases Family: Plant inhibitors of proteinases and amylases Phyre2 PDB 2btc chain I Region: 105 - 124 Aligned: 17 Modelled: 17 Confidence: 6.1% Identity: 24% PDB header:hydrolase/hydrolase inhibitor Chain: I: PDB Molecule:protein (trypsin inhibitor); PDBTitle: bovine trypsin in complex with squash seed inhibitor2 (cucurbita pepo trypsin inhibitor ii) Phyre2 PDB 2noc chain A domain 1 Region: 84 - 106 Aligned: 23 Modelled: 23 Confidence: 5.9% Identity: 30% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2cti chain A Region: 105 - 124 Aligned: 17 Modelled: 17 Confidence: 5.6% Identity: 29% PDB header:proteinase inhibitor (trypsin) Chain: A: PDB Molecule:trypsin inhibitor; PDBTitle: determination of the complete three-dimensional structure2 of the trypsin inhibitor from squash seeds in aqueous3 solution by nuclear magnetic resonance and a combination4 of distance geometry and dynamical simulated annealing Phyre2 1 c2y1bA_ 2 d1vr4a1 3 c3qkbB_ 4 c1y2iC_ 5 d1y2ia_ 6 c2jz7A_ 7 d2gk3a1 8 d2jnaa1 9 c2kxhB_ 10 d1n1ia1 11 d1ob1c1 12 d1b9wa1 13 d2cr9a1 14 d1eyfa_ 15 c2stbI_ 16 c2staI_ 17 d2btci_ 18 c2btcI_ 19 d2noca1 20 c2ctiA_ 21 22 23 24 25

Detailed template information

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

1 c2y1bA_ 100.0 100 PDB header:membrane protein Chain: A: PDB Molecule:putative outer membrane protein, signal; PDBTitle: crystal structure of the e. coli outer membrane lipoprotein2 rcsf 2 d1vr4a1 97.1 24 Fold:Dodecin subunit-like Superfamily:YbjQ-like Family:YbjQ-like 3 c3qkbB_ 96.8 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution 4 c1y2iC_ 96.4 16 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein s0862; PDBTitle: crystal structure of mcsg target apc27401 from shigella2 flexneri 5 d1y2ia_ 96.3 16 Fold:Dodecin subunit-like Superfamily:YbjQ-like Family:YbjQ-like 6 c2jz7A_ 42.6 22 PDB header:selenium-binding protein Chain: A: PDB Molecule:selenium binding protein; PDBTitle: solution nmr structure of selenium-binding protein from2 methanococcus vannielii 7 d2gk3a1 16.7 11 Fold:Flavodoxin-like Superfamily:Class I glutamine amidotransferase-like Family:STM3548-like 8 d2jnaa1 16.6 10 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 9 c2kxhB_ 12.0 28 PDB header:protein binding Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1; PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide 10 d1n1ia1 11.4 38 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:EGF/Laminin Family:Merozoite surface protein 1 (MSP-1) 11 d1ob1c1 10.6 31 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:EGF/Laminin Family:Merozoite surface protein 1 (MSP-1) 12 d1b9wa1 10.4 38 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:EGF/Laminin Family:Merozoite surface protein 1 (MSP-1) 13 d2cr9a1 7.9 19 Fold:WGR domain-like Superfamily:WGR domain-like Family:WGR domain 14 d1eyfa_ 7.3 30 Fold:Ada DNA repair protein, N-terminal domain (N-Ada 10) Superfamily:Ada DNA repair protein, N-terminal domain (N-Ada 10) Family:Ada DNA repair protein, N-terminal domain (N-Ada 10) 15 c2stbI_ 6.9 24 PDB header:hydrolase/hydrolase inhibitor Chain: I: PDB Molecule:protein (trypsin inhibitor); PDBTitle: anionic salmon trypsin in complex with squash seed2 inhibitor (cucurbita pepo trypsin inhibitor ii) 16 c2staI_ 6.3 29 PDB header:hydrolase/hydrolase inhibitor Chain: I: PDB Molecule:protein (trypsin inhibitor); PDBTitle: anionic salmon trypsin in complex with squash seed2 inhibitor (cucurbita maxima trypsin inhibitor i) 17 d2btci_ 6.1 24 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Plant inhibitors of proteinases and amylases Family:Plant inhibitors of proteinases and amylases 18 c2btcI_ 6.1 24 PDB header:hydrolase/hydrolase inhibitor Chain: I: PDB Molecule:protein (trypsin inhibitor); PDBTitle: bovine trypsin in complex with squash seed inhibitor2 (cucurbita pepo trypsin inhibitor ii) 19 d2noca1 5.9 30 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 20 c2ctiA_ 5.6 29 PDB header:proteinase inhibitor (trypsin) Chain: A: PDB Molecule:trypsin inhibitor; PDBTitle: determination of the complete three-dimensional structure2 of the trypsin inhibitor from squash seeds in aqueous3 solution by nuclear magnetic resonance and a combination4 of distance geometry and dynamical simulated annealing 21 c1ctiA_ not modelled 5.6 29 PDB header:proteinase inhibitor (trypsin) Chain: A: PDB Molecule:trypsin inhibitor; PDBTitle: determination of the complete three-dimensional structure2 of the trypsin inhibitor from squash seeds in aqueous3 solution by nuclear magnetic resonance and a combination4 of distance geometry and dynamical simulated annealing 22 c1ppeI_ not modelled 5.6 29 PDB header:hydrolase(serine proteinase) Chain: I: PDB Molecule:trypsin inhibitor cmti-i; PDBTitle: the refined 2.0 angstroms x-ray crystal structure of the2 complex formed between bovine beta-trypsin and cmti-i, a3 trypsin inhibitor from squash seeds (cucurbita maxima):4 topological similarity of the squash seed inhibitors with5 the carboxypeptidase a inhibitor from potatoes 23 c3ctiA_ not modelled 5.6 29 PDB header:proteinase inhibitor (trypsin) Chain: A: PDB Molecule:trypsin inhibitor; PDBTitle: relaxation matrix refinement of the solution structure of2 squash trypsin inhibitor 24 d1mi8a_ not modelled 5.4 30 Fold:Hedgehog/intein (Hint) domain Superfamily:Hedgehog/intein (Hint) domain Family:Intein (protein splicing domain) 25 c3rhtB_ not modelled 5.2 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:(gatase1)-like protein; PDBTitle: crystal structure of type 1 glutamine amidotransferase (gatase1)-like2 protein from planctomyces limnophilus

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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