Secondary structure and disorder prediction

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Sequence		M	N	S	A	F	V	L	V	L	T	V	F	L	V	S	G	E	P	V	D	I	A	V	S	V	H	R	T	M	Q	E	C	M	T	A	A	T	E	Q	K	I	P	G	N	C	Y	P	V	D	K	V	I	H	Q	D	N	I	E	I	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?																														?	?	?	?	?	?		?	?														?	?	?	?
Disorder confidence
		.	.	.
Sequence		A	G	L
Secondary structure
SS confidence
Disorder		?	?	?
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 1wqk chain A Region: 45 - 49 Aligned: 5 Modelled: 5 Confidence: 15.9% Identity: 100% PDB header:toxin Chain: A: PDB Molecule:toxin apetx1; PDBTitle: solution structure of apetx1, a specific peptide inhibitor2 of human ether-a-go-go-related gene potassium channels3 from the venom of the sea anemone anthopleura4 elegantissima: a new fold for an herg toxin Phyre2 PDB 2guy chain A domain 1 Region: 9 - 19 Aligned: 11 Modelled: 11 Confidence: 11.3% Identity: 27% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 2aaa chain A domain 1 Region: 9 - 19 Aligned: 11 Modelled: 11 Confidence: 10.2% Identity: 36% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 2taa chain A domain 1 Region: 9 - 19 Aligned: 11 Modelled: 11 Confidence: 8.7% Identity: 27% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 2qtx chain L Region: 9 - 23 Aligned: 15 Modelled: 15 Confidence: 8.5% Identity: 40% PDB header:rna binding protein Chain: L: PDB Molecule:uncharacterized protein mj1435; PDBTitle: crystal structure of an hfq-like protein from methanococcus2 jannaschii Phyre2 PDB 1kq1 chain W Region: 9 - 28 Aligned: 20 Modelled: 20 Confidence: 7.0% Identity: 20% PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq Phyre2 PDB 1wxn chain A Region: 45 - 49 Aligned: 5 Modelled: 5 Confidence: 6.4% Identity: 60% PDB header:toxin Chain: A: PDB Molecule:toxin apetx2; PDBTitle: solution structure of apetx2, a specific peptide inhibitor2 of asic3 proton-gated channels Phyre2 PDB 2qsd chain B Region: 11 - 51 Aligned: 41 Modelled: 41 Confidence: 6.3% Identity: 27% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of a protein il1583 from idiomarina loihiensis Phyre2 PDB 2hwn chain F Region: 25 - 32 Aligned: 8 Modelled: 8 Confidence: 6.0% Identity: 50% PDB header:transferase Chain: F: PDB Molecule:a kinase binding peptide; PDBTitle: crystal structure of rii alpha dimerization/docking domain of pka2 bound to the d-akap2 peptide Phyre2 PDB 2hwn chain E Region: 25 - 32 Aligned: 8 Modelled: 8 Confidence: 6.0% Identity: 50% PDB header:transferase Chain: E: PDB Molecule:a kinase binding peptide; PDBTitle: crystal structure of rii alpha dimerization/docking domain of pka2 bound to the d-akap2 peptide Phyre2 PDB 2qam chain C domain 1 Region: 42 - 51 Aligned: 10 Modelled: 10 Confidence: 6.0% Identity: 40% Fold: SH3-like barrel Superfamily: Translation proteins SH3-like domain Family: C-terminal domain of ribosomal protein L2 Phyre2 PDB 1p9q chain C domain 3 Region: 57 - 63 Aligned: 7 Modelled: 7 Confidence: 5.9% Identity: 43% Fold: Ferredoxin-like Superfamily: EF-G C-terminal domain-like Family: Hypothetical protein AF0491, C-terminal domain Phyre2 PDB 1qf8 chain A Region: 50 - 63 Aligned: 14 Modelled: 14 Confidence: 5.9% Identity: 29% Fold: Rubredoxin-like Superfamily: Casein kinase II beta subunit Family: Casein kinase II beta subunit Phyre2 PDB 1u1s chain A domain 1 Region: 9 - 28 Aligned: 20 Modelled: 20 Confidence: 5.6% Identity: 15% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Pleiotropic translational regulator Hfq Phyre2 PDB 1t95 chain A domain 3 Region: 57 - 63 Aligned: 7 Modelled: 5 Confidence: 5.6% Identity: 43% Fold: Ferredoxin-like Superfamily: EF-G C-terminal domain-like Family: Hypothetical protein AF0491, C-terminal domain Phyre2 PDB 1w7v chain D Region: 12 - 44 Aligned: 33 Modelled: 33 Confidence: 5.4% Identity: 18% PDB header:hydrolase Chain: D: PDB Molecule:xaa-pro aminopeptidase; PDBTitle: znmg substituted aminopeptidase p from e. coli Phyre2 PDB 2aiv chain A Region: 44 - 50 Aligned: 7 Modelled: 7 Confidence: 5.4% Identity: 100% PDB header:transport protein Chain: A: PDB Molecule:fragment of nucleoporin nup116/nsp116; PDBTitle: multiple conformations in the ligand-binding site of the2 yeast nuclear pore targeting domain of nup116p Phyre2 PDB 2guk chain A domain 1 Region: 26 - 33 Aligned: 8 Modelled: 8 Confidence: 5.2% Identity: 13% Fold: PG1857-like Superfamily: PG1857-like Family: PG1857-like Phyre2 PDB 2i9x chain A domain 1 Region: 2 - 36 Aligned: 35 Modelled: 35 Confidence: 5.0% Identity: 23% Fold: SpoVG-like Superfamily: SpoVG-like Family: SpoVG-like Phyre2 1 c1wqkA_ 2 d2guya1 3 d2aaaa1 4 d2taaa1 5 c2qtxL_ 6 c1kq1W_ 7 c1wxnA_ 8 c2qsdB_ 9 c2hwnF_ 10 c2hwnE_ 11 d2qamc1 12 d1p9qc3 13 d1qf8a_ 14 d1u1sa1 15 d1t95a3 16 c1w7vD_ 17 c2aivA_ 18 d2guka1 19 d2i9xa1

Detailed template information

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

1 c1wqkA_ 15.9 100 PDB header:toxin Chain: A: PDB Molecule:toxin apetx1; PDBTitle: solution structure of apetx1, a specific peptide inhibitor2 of human ether-a-go-go-related gene potassium channels3 from the venom of the sea anemone anthopleura4 elegantissima: a new fold for an herg toxin 2 d2guya1 11.3 27 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 3 d2aaaa1 10.2 36 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 4 d2taaa1 8.7 27 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 5 c2qtxL_ 8.5 40 PDB header:rna binding protein Chain: L: PDB Molecule:uncharacterized protein mj1435; PDBTitle: crystal structure of an hfq-like protein from methanococcus2 jannaschii 6 c1kq1W_ 7.0 20 PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq 7 c1wxnA_ 6.4 60 PDB header:toxin Chain: A: PDB Molecule:toxin apetx2; PDBTitle: solution structure of apetx2, a specific peptide inhibitor2 of asic3 proton-gated channels 8 c2qsdB_ 6.3 27 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of a protein il1583 from idiomarina loihiensis 9 c2hwnF_ 6.0 50 PDB header:transferase Chain: F: PDB Molecule:a kinase binding peptide; PDBTitle: crystal structure of rii alpha dimerization/docking domain of pka2 bound to the d-akap2 peptide 10 c2hwnE_ 6.0 50 PDB header:transferase Chain: E: PDB Molecule:a kinase binding peptide; PDBTitle: crystal structure of rii alpha dimerization/docking domain of pka2 bound to the d-akap2 peptide 11 d2qamc1 6.0 40 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:C-terminal domain of ribosomal protein L2 12 d1p9qc3 5.9 43 Fold:Ferredoxin-like Superfamily:EF-G C-terminal domain-like Family:Hypothetical protein AF0491, C-terminal domain 13 d1qf8a_ 5.9 29 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 14 d1u1sa1 5.6 15 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 15 d1t95a3 5.6 43 Fold:Ferredoxin-like Superfamily:EF-G C-terminal domain-like Family:Hypothetical protein AF0491, C-terminal domain 16 c1w7vD_ 5.4 18 PDB header:hydrolase Chain: D: PDB Molecule:xaa-pro aminopeptidase; PDBTitle: znmg substituted aminopeptidase p from e. coli 17 c2aivA_ 5.4 100 PDB header:transport protein Chain: A: PDB Molecule:fragment of nucleoporin nup116/nsp116; PDBTitle: multiple conformations in the ligand-binding site of the2 yeast nuclear pore targeting domain of nup116p 18 d2guka1 5.2 13 Fold:PG1857-like Superfamily:PG1857-like Family:PG1857-like 19 d2i9xa1 5.0 23 Fold:SpoVG-like Superfamily:SpoVG-like Family:SpoVG-like

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