Secondary structure and disorder prediction

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Sequence		M	R	Q	F	Y	Q	H	Y	F	T	A	T	A	K	L	C	W	L	R	W	L	S	V	P	Q	R	L	T	M	L	E	G	L	M	Q	W	D	D	R	N	S	E	S
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 2icw chain G domain 1 Region: 3 - 9 Aligned: 7 Modelled: 7 Confidence: 11.8% Identity: 71% Fold: Superantigen MAM Superfamily: Superantigen MAM Family: Superantigen MAM Phyre2 PDB 3tbi chain A Region: 21 - 41 Aligned: 21 Modelled: 20 Confidence: 10.5% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:rna polymerase-associated protein gp33; PDBTitle: crystal structure of t4 gp33 bound to e. coli rnap beta-flap domain Phyre2 PDB 2zsh chain B Region: 23 - 34 Aligned: 12 Modelled: 12 Confidence: 7.7% Identity: 50% PDB header:hormone receptor Chain: B: PDB Molecule:della protein gai; PDBTitle: structural basis of gibberellin(ga3)-induced della2 recognition by the gibberellin receptor Phyre2 PDB 2hn8 chain A Region: 15 - 23 Aligned: 9 Modelled: 9 Confidence: 7.5% Identity: 44% PDB header:viral protein Chain: A: PDB Molecule:protein pb1-f2; PDBTitle: structural characterization and oligomerization of pb1-f2,2 a pro-apoptotic influenza a virus protein Phyre2 PDB 1scf chain A Region: 11 - 35 Aligned: 24 Modelled: 25 Confidence: 7.4% Identity: 25% PDB header:hormone/growth factor Chain: A: PDB Molecule:stem cell factor; PDBTitle: human recombinant stem cell factor Phyre2 PDB 1scf chain A Region: 11 - 35 Aligned: 24 Modelled: 25 Confidence: 7.4% Identity: 25% Fold: 4-helical cytokines Superfamily: 4-helical cytokines Family: Short-chain cytokines Phyre2 PDB 1scf chain C Region: 11 - 35 Aligned: 24 Modelled: 25 Confidence: 6.5% Identity: 25% Fold: 4-helical cytokines Superfamily: 4-helical cytokines Family: Short-chain cytokines Phyre2 PDB 1cmr chain A Region: 12 - 27 Aligned: 12 Modelled: 16 Confidence: 6.2% Identity: 83% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 2ds2 chain A Region: 2 - 7 Aligned: 6 Modelled: 6 Confidence: 6.2% Identity: 83% PDB header:plant protein Chain: A: PDB Molecule:sweet protein mabinlin-2 chain a; PDBTitle: crystal structure of mabinlin ii Phyre2 PDB 1o7n chain A domain 2 Region: 1 - 8 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 50% Fold: TBP-like Superfamily: Bet v1-like Family: Ring hydroxylating alpha subunit catalytic domain Phyre2 PDB 1l8n chain A domain 2 Region: 16 - 20 Aligned: 5 Modelled: 5 Confidence: 5.9% Identity: 80% Fold: Zincin-like Superfamily: beta-N-acetylhexosaminidase-like domain Family: alpha-D-glucuronidase, N-terminal domain Phyre2 PDB 3eno chain C Region: 17 - 23 Aligned: 7 Modelled: 7 Confidence: 5.4% Identity: 43% PDB header:hydrolase/unknown function Chain: C: PDB Molecule:uncharacterized protein pf2011; PDBTitle: crystal structure of pyrococcus furiosus pcc1 in complex2 with thermoplasma acidophilum kae1 Phyre2 1 d2icwg1 2 c3tbiA_ 3 c2zshB_ 4 c2hn8A_ 5 c1scfA_ 6 d1scfa_ 7 d1scfc_ 8 d1cmra_ 9 c2ds2A_ 10 d1o7na2 11 d1l8na2 12 c3enoC_

Detailed template information

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

1 d2icwg1 11.8 71 Fold:Superantigen MAM Superfamily:Superantigen MAM Family:Superantigen MAM 2 c3tbiA_ 10.5 19 PDB header:transcription Chain: A: PDB Molecule:rna polymerase-associated protein gp33; PDBTitle: crystal structure of t4 gp33 bound to e. coli rnap beta-flap domain 3 c2zshB_ 7.7 50 PDB header:hormone receptor Chain: B: PDB Molecule:della protein gai; PDBTitle: structural basis of gibberellin(ga3)-induced della2 recognition by the gibberellin receptor 4 c2hn8A_ 7.5 44 PDB header:viral protein Chain: A: PDB Molecule:protein pb1-f2; PDBTitle: structural characterization and oligomerization of pb1-f2,2 a pro-apoptotic influenza a virus protein 5 c1scfA_ 7.4 25 PDB header:hormone/growth factor Chain: A: PDB Molecule:stem cell factor; PDBTitle: human recombinant stem cell factor 6 d1scfa_ 7.4 25 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Short-chain cytokines 7 d1scfc_ 6.5 25 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Short-chain cytokines 8 d1cmra_ 6.2 83 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 9 c2ds2A_ 6.2 83 PDB header:plant protein Chain: A: PDB Molecule:sweet protein mabinlin-2 chain a; PDBTitle: crystal structure of mabinlin ii 10 d1o7na2 6.2 50 Fold:TBP-like Superfamily:Bet v1-like Family:Ring hydroxylating alpha subunit catalytic domain 11 d1l8na2 5.9 80 Fold:Zincin-like Superfamily:beta-N-acetylhexosaminidase-like domain Family:alpha-D-glucuronidase, N-terminal domain 12 c3enoC_ 5.4 43 PDB header:hydrolase/unknown function Chain: C: PDB Molecule:uncharacterized protein pf2011; PDBTitle: crystal structure of pyrococcus furiosus pcc1 in complex2 with thermoplasma acidophilum kae1

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