Secondary structure and disorder prediction

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Sequence

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N

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A

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K

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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 3bdr chain A Region: 12 - 21 Aligned: 10 Modelled: 10 Confidence: 37.0% Identity: 60% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ycf58 protein; PDBTitle: crystal structure of fatty acid-binding protein-like ycf582 from thermosynecoccus elongatus. northeast structural3 genomics consortium target ter13. Phyre2 PDB 2y69 chain X Region: 9 - 27 Aligned: 19 Modelled: 19 Confidence: 15.1% Identity: 32% PDB header:electron transport Chain: X: PDB Molecule:cytochrome c oxidase polypeptide 7b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1v54 chain K Region: 9 - 27 Aligned: 19 Modelled: 19 Confidence: 15.1% Identity: 32% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIb Family: Mitochondrial cytochrome c oxidase subunit VIIb Phyre2 PDB 2yum chain A Region: 5 - 27 Aligned: 23 Modelled: 23 Confidence: 10.8% Identity: 17% PDB header:transcription Chain: A: PDB Molecule:zinc finger zz-type-containing protein 3; PDBTitle: solution structure of the myb-like dna-binding domain of2 human zzz3 protein Phyre2 PDB 1zec chain A Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 7.8% Identity: 71% PDB header:viral peptide Chain: A: PDB Molecule:nef1-25; PDBTitle: nmr solution structure of nef1-25, 20 structures Phyre2 PDB 1h6v chain A domain 3 Region: 16 - 26 Aligned: 11 Modelled: 11 Confidence: 7.7% Identity: 36% Fold: CO dehydrogenase flavoprotein C-domain-like Superfamily: FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family: FAD/NAD-linked reductases, dimerisation (C-terminal) domain Phyre2 PDB 1x41 chain A domain 1 Region: 11 - 27 Aligned: 17 Modelled: 17 Confidence: 7.4% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Homeodomain Phyre2 PDB 1fdf chain A Region: 12 - 22 Aligned: 11 Modelled: 11 Confidence: 6.7% Identity: 55% PDB header:signaling protein Chain: A: PDB Molecule:rhodopsin; PDBTitle: helix 7 bovine rhodopsin Phyre2 PDB 1uw4 chain A Region: 1 - 23 Aligned: 22 Modelled: 23 Confidence: 6.4% Identity: 14% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Smg-4/UPF3 Phyre2 PDB 1wgx chain A Region: 10 - 27 Aligned: 18 Modelled: 18 Confidence: 6.1% Identity: 28% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 2wj8 chain N Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 6.0% Identity: 64% PDB header:rna binding protein/rna Chain: N: PDB Molecule:nucleoprotein; PDBTitle: respiratory syncitial virus ribonucleoprotein Phyre2 1 c3bdrA_ 2 c2y69X_ 3 d1v54k_ 4 c2yumA_ 5 c1zecA_ 6 d1h6va3 7 d1x41a1 8 c1fdfA_ 9 d1uw4a_ 10 d1wgxa_ 11 c2wj8N_

Detailed template information

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

1 c3bdrA_ 37.0 60 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ycf58 protein; PDBTitle: crystal structure of fatty acid-binding protein-like ycf582 from thermosynecoccus elongatus. northeast structural3 genomics consortium target ter13. 2 c2y69X_ 15.1 32 PDB header:electron transport Chain: X: PDB Molecule:cytochrome c oxidase polypeptide 7b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 3 d1v54k_ 15.1 32 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIb Family:Mitochondrial cytochrome c oxidase subunit VIIb 4 c2yumA_ 10.8 17 PDB header:transcription Chain: A: PDB Molecule:zinc finger zz-type-containing protein 3; PDBTitle: solution structure of the myb-like dna-binding domain of2 human zzz3 protein 5 c1zecA_ 7.8 71 PDB header:viral peptide Chain: A: PDB Molecule:nef1-25; PDBTitle: nmr solution structure of nef1-25, 20 structures 6 d1h6va3 7.7 36 Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain 7 d1x41a1 7.4 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 8 c1fdfA_ 6.7 55 PDB header:signaling protein Chain: A: PDB Molecule:rhodopsin; PDBTitle: helix 7 bovine rhodopsin 9 d1uw4a_ 6.4 14 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Smg-4/UPF3 10 d1wgxa_ 6.1 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 11 c2wj8N_ 6.0 64 PDB header:rna binding protein/rna Chain: N: PDB Molecule:nucleoprotein; PDBTitle: respiratory syncitial virus ribonucleoprotein

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