Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	I	T	A	T	V	L	L	A	F	G	M	S	M	D	A	F	A	A	S	I	G	K	G	A	T	L	H	K	P	K	F	S	E	A	L	R	T	G	L	I	F	G	A	V	E	T	L	T	P	L	I	G	W	G	M	G	M	L
Secondary structure
SS confidence
Disorder		?	?																								?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	S	R	F	V	L	E	W	N	H	W	I	A	F	V	L	L	I	F	L	G	G	R	M	I	I	E	G	F	R	G	A	D	D	E	D	E	E	P	R	R	R	H	G	F	W	L	L	V	T	T	A	I	A	T	S	L	D	A	M
Secondary structure
SS confidence
Disorder																																	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	V	G	V	G	L	A	F	L	Q	V	N	I	I	A	T	A	L	A	I	G	C	A	T	L	I	M	S	T	L	G	M	M	V	G	R	F	I	G	S	I	I	G	K	K	A	E	I	L	G	G	L	V	L	I	G	I	G	V	Q
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		I	L	W	T	H	F	H	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 1upt chain D Region: 180 - 188 Aligned: 9 Modelled: 6 Confidence: 19.7% Identity: 22% Fold: GRIP domain Superfamily: GRIP domain Family: GRIP domain Phyre2 PDB 2j5d chain A Region: 137 - 159 Aligned: 23 Modelled: 23 Confidence: 18.8% Identity: 22% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles Phyre2 PDB 2ka2 chain B Region: 137 - 158 Aligned: 22 Modelled: 22 Confidence: 18.0% Identity: 23% PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints Phyre2 PDB 2ka1 chain A Region: 137 - 158 Aligned: 22 Modelled: 22 Confidence: 18.0% Identity: 23% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles Phyre2 PDB 2ka2 chain A Region: 137 - 158 Aligned: 22 Modelled: 22 Confidence: 18.0% Identity: 23% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints Phyre2 PDB 2ka1 chain B Region: 137 - 158 Aligned: 22 Modelled: 22 Confidence: 18.0% Identity: 23% PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles Phyre2 PDB 3rko chain K Region: 1 - 104 Aligned: 98 Modelled: 104 Confidence: 16.0% Identity: 9% PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3few chain X Region: 112 - 164 Aligned: 53 Modelled: 53 Confidence: 6.6% Identity: 19% PDB header:immune system Chain: X: PDB Molecule:colicin s4; PDBTitle: structure and function of colicin s4, a colicin with a2 duplicated receptor binding domain Phyre2 PDB 3hfx chain A Region: 3 - 95 Aligned: 89 Modelled: 93 Confidence: 6.4% Identity: 6% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 1a87 chain A Region: 107 - 167 Aligned: 61 Modelled: 61 Confidence: 6.1% Identity: 15% Fold: Toxins' membrane translocation domains Superfamily: Colicin Family: Colicin Phyre2 PDB 1a87 chain A Region: 107 - 167 Aligned: 61 Modelled: 61 Confidence: 6.1% Identity: 15% PDB header:bacteriocin Chain: A: PDB Molecule:colicin n; PDBTitle: colicin n Phyre2 1 d1uptd_ 2 c2j5dA_ 3 c2ka2B_ 4 c2ka1A_ 5 c2ka2A_ 6 c2ka1B_ 7 c3rkoK_ 8 c3fewX_ 9 c3hfxA_ 10 d1a87a_ 11 c1a87A_

Detailed template information

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

1 d1uptd_ 19.7 22 Fold:GRIP domain Superfamily:GRIP domain Family:GRIP domain 2 c2j5dA_ 18.8 22 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles 3 c2ka2B_ 18.0 23 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 4 c2ka1A_ 18.0 23 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 5 c2ka2A_ 18.0 23 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 6 c2ka1B_ 18.0 23 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 7 c3rkoK_ 16.0 9 PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 8 c3fewX_ 6.6 19 PDB header:immune system Chain: X: PDB Molecule:colicin s4; PDBTitle: structure and function of colicin s4, a colicin with a2 duplicated receptor binding domain 9 c3hfxA_ 6.4 6 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 10 d1a87a_ 6.1 15 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 11 c1a87A_ 6.1 15 PDB header:bacteriocin Chain: A: PDB Molecule:colicin n; PDBTitle: colicin n

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