Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	H	V	L	N	I	L	W	V	V	F	G	I	G	L	M	L	V	L	N	L	K	F	K	I	N	S	M	V	A	L	L	V	A	A	L	S	V	G	M	L	A	G	M	D	L	M	S	L	L	H	T	M	K	A	G	F	G	N	T
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	G	E	L	A	I	I	V	V	F	G	A	V	I	G	K	L	M	V	D	S	G	A	A	H	Q	I	A	H	T	L	L	A	R	L	G	L	R	Y	V	Q	L	S	V	I	I	I	G	L	I	F	G	L	A	M	F	Y	E	V	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	I	M	L	A	P	L	V	I	V	I	A	A	E	A	K	I	P	F	L	K	L	A	I	P	A	V	A	A	A	T	T	A	H	S	L	F	P	P	Q	P	G	P	V	A	L	V	N	A	Y	G	A	D	M	G	M	V	Y	I	Y
Secondary structure
SS confidence
Disorder																?	?	?																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	V	L	V	T	I	P	S	V	I	C	A	G	L	I	L	P	K	F	L	G	N	L	E	R	P	T	P	S	F	L	K	A	D	Q	P	V	D	M	N	N	L	P	S	F	G	V	S	I	L	V	P	L	I	P	A	I	I	M	I
Secondary structure
SS confidence
Disorder																													?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	T	T	I	A	N	I	W	L	V	K	D	T	P	A	W	E	V	V	N	F	I	G	S	S	P	I	A	M	F	I	A	M	V	V	A	F	V	L	F	G	T	A	R	G	H	D	M	Q	W	V	M	N	A	F	E	S	A	V	K
Secondary structure
SS confidence
Disorder								?	?		?		?	?	?																												?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		S	I	A	M	V	I	L	I	I	G	A	G	G	V	L	K	Q	T	I	I	D	T	G	I	G	D	T	I	G	M	L	M	S	H	G	N	I	S	P	Y	I	M	A	W	L	I	T	V	L	I	R	L	A	T	G	Q	G	V	V	S
Secondary structure
SS confidence
Disorder																								?										?		?	?	?	?	?															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		A	M	T	A	A	G	I	I	S	A	A	I	L	D	P	A	T	G	Q	L	V	G	V	N	P	A	L	L	V	L	A	T	A	A	G	S	N	T	L	T	H	I	N	D	A	S	F	W	L	F	K	G	Y	F	D	L	S	V	K	D
Secondary structure
SS confidence
Disorder														?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.
Sequence		T	L	K	T	W	G	L	L	E	L	V	N	S	V	V	G	L	I	I	V	L	I	I	S	M	V	A
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 2w8a chain C Region: 27 - 334 Aligned: 277 Modelled: 290 Confidence: 28.7% Identity: 11% PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate Phyre2 PDB 1fft chain B domain 2 Region: 174 - 239 Aligned: 66 Modelled: 66 Confidence: 9.6% Identity: 11% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2knc chain A Region: 176 - 217 Aligned: 42 Modelled: 42 Confidence: 8.8% Identity: 14% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2jln chain A Region: 181 - 219 Aligned: 39 Modelled: 39 Confidence: 7.4% Identity: 0% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 1 c2w8aC_ 2 d1fftb2 3 c2kncA_ 4 c2jlnA_

Detailed template information

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

1 c2w8aC_ 28.7 11 PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate 2 d1fftb2 9.6 11 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 3 c2kncA_ 8.8 14 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 4 c2jlnA_ 7.4 0 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter

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