Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	P	E	S	V	M	M	M	G	T	E	A	M	K	V	A	L	A	L	A	A	P	L	L	L	V	A	L	V	T	G	L	I	I	S	I	L	Q	A	A	T	Q	I	N	E	M	T	L	S	F	I	P	K	I	I	A	V	F	I
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.
Sequence		A	I	I	I	A	G	P	W	M	L	N	L	L	L	D	Y	V	R	T	L	F	T	N	L	P	Y	I	I	G
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 2jx5 chain A Region: 44 - 51 Aligned: 8 Modelled: 8 Confidence: 9.8% Identity: 38% PDB header:ribosomal protein Chain: A: PDB Molecule:glub(s27a); PDBTitle: solution structure of the ubiquitin domain n-terminal to2 the s27a ribosomal subunit of giardia lamblia Phyre2 PDB 2y69 chain Z Region: 55 - 76 Aligned: 22 Modelled: 22 Confidence: 9.0% Identity: 23% PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1v54 chain M Region: 55 - 76 Aligned: 22 Modelled: 22 Confidence: 8.8% Identity: 23% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Phyre2 PDB 3nzz chain A Region: 34 - 53 Aligned: 20 Modelled: 20 Confidence: 6.9% Identity: 55% PDB header:cell invasion Chain: A: PDB Molecule:cell invasion protein sipd; PDBTitle: crystal structure of the salmonella type iii secretion system tip2 protein sipd Phyre2 PDB 1g2c chain N Region: 40 - 54 Aligned: 15 Modelled: 15 Confidence: 6.1% Identity: 47% PDB header:viral protein Chain: N: PDB Molecule:fusion protein (f); PDBTitle: human respiratory syncytial virus fusion protein core Phyre2 PDB 1sdi chain A Region: 36 - 46 Aligned: 11 Modelled: 11 Confidence: 5.2% Identity: 27% Fold: YcfC-like Superfamily: YcfC-like Family: YcfC-like Phyre2 PDB 2goh chain A Region: 26 - 38 Aligned: 13 Modelled: 13 Confidence: 5.0% Identity: 54% PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: three-dimensional structure of the trans-membrane domain of2 vpu from hiv-1 in aligned phospholipid bicelles Phyre2 PDB 2gof chain A Region: 26 - 38 Aligned: 13 Modelled: 13 Confidence: 5.0% Identity: 54% PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: three-dimensional structure of the trans-membrane domain of2 vpu from hiv-1 in aligned phospholipid bicelles Phyre2 PDB 1pje chain A Region: 26 - 38 Aligned: 13 Modelled: 13 Confidence: 5.0% Identity: 54% PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: structure of the channel-forming trans-membrane domain of2 virus protein "u"(vpu) from hiv-1 Phyre2 PDB 1pi7 chain A Region: 26 - 38 Aligned: 13 Modelled: 13 Confidence: 5.0% Identity: 54% PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: structure of the channel-forming trans-membrane domain of2 virus protein "u" (vpu) from hiv-1 Phyre2 1 c2jx5A_ 2 c2y69Z_ 3 d1v54m_ 4 c3nzzA_ 5 c1g2cN_ 6 d1sdia_ 7 c2gohA_ 8 c2gofA_ 9 c1pjeA_ 10 c1pi7A_

Detailed template information

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

1 c2jx5A_ 9.8 38 PDB header:ribosomal protein Chain: A: PDB Molecule:glub(s27a); PDBTitle: solution structure of the ubiquitin domain n-terminal to2 the s27a ribosomal subunit of giardia lamblia 2 c2y69Z_ 9.0 23 PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 3 d1v54m_ 8.8 23 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) 4 c3nzzA_ 6.9 55 PDB header:cell invasion Chain: A: PDB Molecule:cell invasion protein sipd; PDBTitle: crystal structure of the salmonella type iii secretion system tip2 protein sipd 5 c1g2cN_ 6.1 47 PDB header:viral protein Chain: N: PDB Molecule:fusion protein (f); PDBTitle: human respiratory syncytial virus fusion protein core 6 d1sdia_ 5.2 27 Fold:YcfC-like Superfamily:YcfC-like Family:YcfC-like 7 c2gohA_ 5.0 54 PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: three-dimensional structure of the trans-membrane domain of2 vpu from hiv-1 in aligned phospholipid bicelles 8 c2gofA_ 5.0 54 PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: three-dimensional structure of the trans-membrane domain of2 vpu from hiv-1 in aligned phospholipid bicelles 9 c1pjeA_ 5.0 54 PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: structure of the channel-forming trans-membrane domain of2 virus protein "u"(vpu) from hiv-1 10 c1pi7A_ 5.0 54 PDB header:viral protein Chain: A: PDB Molecule:vpu protein; PDBTitle: structure of the channel-forming trans-membrane domain of2 virus protein "u" (vpu) from hiv-1

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

---

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