Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	A	G	K	I	T	A	A	I	S	G	A	F	L	L	L	I	V	V	A	I	I	L	I	A	T	F	D	W	N	R	L	K	P	T	I	N	Q	K	V	S	A	E	L	N	R	P	F	A	I	R	G	D	L	G	V	V	W
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		E	R	Q	K	Q	E	T	G	W	R	S	W	V	P	W	P	H	V	H	A	E	D	I	I	L	G	N	P	P	D	I	P	E	V	T	M	V	H	L	P	R	V	E	A	T	L	A	P	L	A	L	L	T	K	T	V	W	L	P	W
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?	?	?																	?	?	?	?	?	?		?																		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	K	L	E	K	P	D	A	R	L	I	R	L	S	E	K	N	N	N	W	T	F	N	L	A	N	D	D	N	K	D	A	N	A	K	P	S	A	W	S	F	R	L	D	N	I	L	F	D	Q	G	R	I	A	I	D	D	K	V	S
Secondary structure
SS confidence
Disorder																		?					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?						?		?												?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		K	A	D	L	E	I	F	V	D	P	L	G	K	P	L	P	F	S	E	V	T	G	S	K	G	K	A	D	K	E	K	V	G	D	Y	V	F	G	L	K	A	Q	G	R	Y	N	G	E	P	L	T	G	T	G	K	I	G	G	M	L
Secondary structure
SS confidence
Disorder		?										?	?	?	?	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																	?					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		A	L	R	G	E	G	T	P	F	P	V	Q	A	D	F	R	S	G	N	T	R	V	A	F	D	G	V	V	N	D	P	M	K	M	G	G	V	D	L	R	L	K	F	S	G	D	S	L	G	D	L	Y	E	L	T	G	V	L	L	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?								?			?												?	?		?		?																			?			?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		D	T	P	P	F	E	T	D	G	R	L	V	A	K	I	D	T	E	K	S	S	V	F	D	Y	R	G	F	N	G	R	I	G	D	S	D	I	H	G	S	L	V	Y	T	T	G	K	P	R	P	K	L	E	G	D	V	E	S	R	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?						?	?	?		?	?	?	?	?								?																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		L	R	L	A	D	L	G	P	L	I	G	V	D	S	G	K	G	A	E	K	S	K	R	S	E	Q	K	K	G	E	K	S	V	Q	P	A	G	K	V	L	P	Y	D	R	F	E	T	D	K	W	D	V	M	D	A	D	V	R	F	K
Secondary structure
SS confidence
Disorder								?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		G	R	R	I	E	H	G	S	S	L	P	I	S	D	L	S	T	H	I	I	L	K	N	A	D	L	R	L	Q	P	L	K	F	G	M	A	G	G	S	I	A	A	N	I	H	L	E	G	D	K	K	P	M	Q	G	R	A	D	I	Q
Secondary structure
SS confidence
Disorder					?	?	?	?	?																								?	?		?													?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		A	R	R	L	K	L	K	E	L	M	P	D	V	E	L	M	Q	K	T	L	G	E	M	N	G	D	A	E	L	R	G	S	G	N	S	V	A	A	L	L	G	N	S	N	G	N	L	K	L	L	M	N	D	G	L	V	S	R	N	L
Secondary structure
SS confidence
Disorder														?	?	?	?	?	?	?	?																																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600
Sequence		M	E	I	V	G	L	N	V	G	N	Y	I	V	G	A	I	F	G	D	D	E	V	R	V	N	C	A	A	A	N	L	N	I	A	N	G	V	A	R	P	Q	I	F	A	F	D	T	E	N	A	L	I	N	V	T	G	T	A	S	F
Secondary structure
SS confidence
Disorder						?	?							?	?	?	?	?	?	?	?	?	?		?	?																?	?	?				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	610	.	.	.	.	.	.	.	.	.	620	.	.	.	.	.	.	.	.	.	630	.	.	.	.	.	.	.	.	.	640	.	.	.	.	.	.	.	.	.	650	.	.	.	.	.	.	.	.	.	660
Sequence		A	S	E	Q	L	D	L	T	I	D	P	E	S	K	G	I	R	I	I	T	L	R	S	P	L	Y	V	R	G	T	F	K	N	P	Q	A	G	V	K	A	G	P	L	I	A	R	G	A	V	A	A	A	L	A	T	L	V	T	P	A
Secondary structure
SS confidence
Disorder													?	?	?	?	?	?	?	?	?	?	?	?											?					?																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	670	.	.	.	.	.	.	.	.	.	680	.	.	.	.	.	.
Sequence		A	A	L	L	A	L	I	S	P	S	E	G	E	A	N	Q	C	R	T	I	L	S	Q	M	K	K
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 1w8x chain P Region: 1 - 24 Aligned: 23 Modelled: 24 Confidence: 67.5% Identity: 22% PDB header:virus Chain: P: PDB Molecule:protein p16; PDBTitle: structural analysis of prd1 Phyre2 PDB 1v54 chain G Region: 1 - 21 Aligned: 21 Modelled: 21 Confidence: 28.4% Identity: 10% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIa Family: Mitochondrial cytochrome c oxidase subunit VIa Phyre2 PDB 1x4q chain A Region: 30 - 47 Aligned: 18 Modelled: 18 Confidence: 13.5% Identity: 33% PDB header:rna binding protein Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3; PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3) Phyre2 PDB 1wx4 chain B Region: 120 - 138 Aligned: 19 Modelled: 19 Confidence: 8.3% Identity: 5% PDB header:oxidoreductase/metal transport Chain: B: PDB Molecule:melc; PDBTitle: crystal structure of the oxy-form of the copper-bound streptomyces2 castaneoglobisporus tyrosinase complexed with a caddie protein3 prepared by the addition of dithiothreitol Phyre2 PDB 3cx5 chain C domain 2 Region: 3 - 47 Aligned: 45 Modelled: 45 Confidence: 7.4% Identity: 7% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1m56 chain D Region: 1 - 21 Aligned: 21 Modelled: 21 Confidence: 6.0% Identity: 14% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 1 c1w8xP_ 2 d1v54g_ 3 c1x4qA_ 4 c1wx4B_ 5 d3cx5c2 6 d1m56d_

Detailed template information

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

1 c1w8xP_ 67.5 22 PDB header:virus Chain: P: PDB Molecule:protein p16; PDBTitle: structural analysis of prd1 2 d1v54g_ 28.4 10 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIa Family:Mitochondrial cytochrome c oxidase subunit VIa 3 c1x4qA_ 13.5 33 PDB header:rna binding protein Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3; PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3) 4 c1wx4B_ 8.3 5 PDB header:oxidoreductase/metal transport Chain: B: PDB Molecule:melc; PDBTitle: crystal structure of the oxy-form of the copper-bound streptomyces2 castaneoglobisporus tyrosinase complexed with a caddie protein3 prepared by the addition of dithiothreitol 5 d3cx5c2 7.4 7 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 6 d1m56d_ 6.0 14 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV

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