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

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Q

G

N

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S

N

N

S

A

P

E

G

T

S

E

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A

K

I

T

R

Q

I

Q

V

L

T

E

K

L

G

K

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S

E

E

G

M

T

T

Q

Q

K

K

E

M

A

A

L

V

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

Sequence

Q

K

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S

L

W

A

Q

L

E

Q

L

L

R

Q

Q

A

E

K

K

N

E

D

A

T

V

Q

P

D

K

K

E

E

K

K

D

D

T

N

T

A

G

T

I

D

I

Y

V

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 3bhp chain A Region: 39 - 75 Aligned: 37 Modelled: 37 Confidence: 40.4% Identity: 19% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: crystal structure of upf0291 protein ynzc from bacillus2 subtilis at resolution 2.0 a. northeast structural3 genomics consortium target sr384 Phyre2 PDB 1t08 chain B Region: 44 - 79 Aligned: 36 Modelled: 36 Confidence: 32.0% Identity: 36% Fold: beta-catenin-interacting protein ICAT Superfamily: beta-catenin-interacting protein ICAT Family: beta-catenin-interacting protein ICAT Phyre2 PDB 1m1e chain B Region: 44 - 85 Aligned: 42 Modelled: 42 Confidence: 25.8% Identity: 33% Fold: beta-catenin-interacting protein ICAT Superfamily: beta-catenin-interacting protein ICAT Family: beta-catenin-interacting protein ICAT Phyre2 PDB 1st6 chain A domain 5 Region: 13 - 88 Aligned: 76 Modelled: 76 Confidence: 18.4% Identity: 16% Fold: Four-helical up-and-down bundle Superfamily: alpha-catenin/vinculin-like Family: alpha-catenin/vinculin Phyre2 PDB 1luj chain B Region: 44 - 79 Aligned: 36 Modelled: 36 Confidence: 18.2% Identity: 36% Fold: beta-catenin-interacting protein ICAT Superfamily: beta-catenin-interacting protein ICAT Family: beta-catenin-interacting protein ICAT Phyre2 PDB 2vn2 chain B Region: 65 - 84 Aligned: 20 Modelled: 20 Confidence: 13.8% Identity: 40% PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 Phyre2 PDB 1uix chain A Region: 22 - 82 Aligned: 59 Modelled: 61 Confidence: 13.4% Identity: 24% PDB header:transferase Chain: A: PDB Molecule:rho-associated kinase; PDBTitle: coiled-coil structure of the rhoa-binding domain in rho-2 kinase Phyre2 PDB 3lay chain F Region: 48 - 93 Aligned: 46 Modelled: 46 Confidence: 13.1% Identity: 20% PDB header:metal binding protein Chain: F: PDB Molecule:zinc resistance-associated protein; PDBTitle: alpha-helical barrel formed by the decamer of the zinc resistance-2 associated protein (stm4172) from salmonella enterica subsp. enterica3 serovar typhimurium str. lt2 Phyre2 PDB 2jvd chain A Region: 39 - 66 Aligned: 28 Modelled: 28 Confidence: 11.1% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the folded n-terminal fragment of2 upf0291 protein ynzc from bacillus subtilis. northeast3 structural genomics target sr384-1-46 Phyre2 PDB 2fup chain A domain 1 Region: 23 - 77 Aligned: 52 Modelled: 55 Confidence: 10.9% Identity: 13% Fold: STAT-like Superfamily: FlgN-like Family: FlgN-like Phyre2 PDB 2fup chain A Region: 23 - 77 Aligned: 52 Modelled: 55 Confidence: 10.9% Identity: 13% PDB header:biosynthetic protein Chain: A: PDB Molecule:hypothetical protein pa3352; PDBTitle: crystal structure of a putative flagella synthesis protein flgn2 (pa3352) from pseudomonas aeruginosa at 1.48 a resolution Phyre2 PDB 1rh4 chain A Region: 52 - 69 Aligned: 18 Modelled: 18 Confidence: 7.8% Identity: 56% PDB header:coiled coil Chain: A: PDB Molecule:right-handed coiled coil tetramer; PDBTitle: rh4 designed right-handed coiled coil tetramer Phyre2 PDB 3qsq chain A Region: 9 - 21 Aligned: 13 Modelled: 13 Confidence: 7.0% Identity: 38% PDB header:viral protein Chain: A: PDB Molecule:capsid polyprotein; PDBTitle: crystal structure of the projection domain of the human astrovirus2 capsid protein Phyre2 PDB 1hbw chain A Region: 64 - 76 Aligned: 13 Modelled: 13 Confidence: 7.0% Identity: 46% PDB header:transcriptional activator Chain: A: PDB Molecule:regulatory protein gal4; PDBTitle: solution nmr structure of the dimerization domain of the2 yeast transcriptional activator gal4 (residues 50-106) Phyre2 PDB 1s1h chain O Region: 34 - 64 Aligned: 31 Modelled: 31 Confidence: 6.9% Identity: 16% PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein s13; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. Phyre2 PDB 1nb4 chain A Region: 44 - 97 Aligned: 54 Modelled: 54 Confidence: 5.7% Identity: 24% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 3aap chain A Region: 56 - 108 Aligned: 53 Modelled: 53 Confidence: 5.5% Identity: 26% PDB header:hydrolase Chain: A: PDB Molecule:ectonucleoside triphosphate diphosphohydrolase i; PDBTitle: crystal structure of lp1ntpdase from legionella pneumophila Phyre2 1 c3bhpA_ 2 d1t08b_ 3 d1m1eb_ 4 d1st6a5 5 d1lujb_ 6 c2vn2B_ 7 c1uixA_ 8 c3layF_ 9 c2jvdA_ 10 d2fupa1 11 c2fupA_ 12 c1rh4A_ 13 c3qsqA_ 14 c1hbwA_ 15 c1s1hO_ 16 d1nb4a_ 17 c3aapA_

Detailed template information

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

1 c3bhpA_ 40.4 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: crystal structure of upf0291 protein ynzc from bacillus2 subtilis at resolution 2.0 a. northeast structural3 genomics consortium target sr384 2 d1t08b_ 32.0 36 Fold:beta-catenin-interacting protein ICAT Superfamily:beta-catenin-interacting protein ICAT Family:beta-catenin-interacting protein ICAT 3 d1m1eb_ 25.8 33 Fold:beta-catenin-interacting protein ICAT Superfamily:beta-catenin-interacting protein ICAT Family:beta-catenin-interacting protein ICAT 4 d1st6a5 18.4 16 Fold:Four-helical up-and-down bundle Superfamily:alpha-catenin/vinculin-like Family:alpha-catenin/vinculin 5 d1lujb_ 18.2 36 Fold:beta-catenin-interacting protein ICAT Superfamily:beta-catenin-interacting protein ICAT Family:beta-catenin-interacting protein ICAT 6 c2vn2B_ 13.8 40 PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 7 c1uixA_ 13.4 24 PDB header:transferase Chain: A: PDB Molecule:rho-associated kinase; PDBTitle: coiled-coil structure of the rhoa-binding domain in rho-2 kinase 8 c3layF_ 13.1 20 PDB header:metal binding protein Chain: F: PDB Molecule:zinc resistance-associated protein; PDBTitle: alpha-helical barrel formed by the decamer of the zinc resistance-2 associated protein (stm4172) from salmonella enterica subsp. enterica3 serovar typhimurium str. lt2 9 c2jvdA_ 11.1 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the folded n-terminal fragment of2 upf0291 protein ynzc from bacillus subtilis. northeast3 structural genomics target sr384-1-46 10 d2fupa1 10.9 13 Fold:STAT-like Superfamily:FlgN-like Family:FlgN-like 11 c2fupA_ 10.9 13 PDB header:biosynthetic protein Chain: A: PDB Molecule:hypothetical protein pa3352; PDBTitle: crystal structure of a putative flagella synthesis protein flgn2 (pa3352) from pseudomonas aeruginosa at 1.48 a resolution 12 c1rh4A_ 7.8 56 PDB header:coiled coil Chain: A: PDB Molecule:right-handed coiled coil tetramer; PDBTitle: rh4 designed right-handed coiled coil tetramer 13 c3qsqA_ 7.0 38 PDB header:viral protein Chain: A: PDB Molecule:capsid polyprotein; PDBTitle: crystal structure of the projection domain of the human astrovirus2 capsid protein 14 c1hbwA_ 7.0 46 PDB header:transcriptional activator Chain: A: PDB Molecule:regulatory protein gal4; PDBTitle: solution nmr structure of the dimerization domain of the2 yeast transcriptional activator gal4 (residues 50-106) 15 c1s1hO_ 6.9 16 PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein s13; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. 16 d1nb4a_ 5.7 24 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 17 c3aapA_ 5.5 26 PDB header:hydrolase Chain: A: PDB Molecule:ectonucleoside triphosphate diphosphohydrolase i; PDBTitle: crystal structure of lp1ntpdase from legionella pneumophila

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