Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	T	L	T	L	V	L	T	A	V	G	S	V	L	L	L	L	F	L	V	M	K	A	R	M	H	A	F	L	A	L	M	V	V	S	M	G	A	G	L	F	S	G	M	P	L	D	K	I	A	A	T	M	E	K	G	M	G	G
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	L	G	F	L	A	V	V	V	A	L	G	A	M	F	G	K	I	L	H	E	T	G	A	V	D	Q	I	A	V	K	M	L	K	S	F	G	H	S	R	A	H	Y	A	I	G	L	A	G	L	V	C	A	L	P	L	F	F	E	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	I	V	L	L	I	S	V	A	F	S	M	A	R	H	T	G	T	N	L	V	K	L	V	I	P	L	F	A	G	V	A	A	A	A	A	F	L	V	P	G	P	A	P	M	L	L	A	S	Q	M	N	A	D	F	G	W	M	I	L
Secondary structure
SS confidence
Disorder																	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	G	L	C	A	A	I	P	G	M	I	I	A	G	P	L	W	G	N	F	I	S	R	Y	V	E	L	H	I	P	D	D	I	S	E	P	H	L	G	E	G	K	M	P	S	F	G	F	S	L	S	L	I	L	L	P	L	V	L	V
Secondary structure
SS confidence
Disorder																							?							?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	L	K	T	I	A	A	R	F	V	P	E	G	S	T	A	Y	E	W	F	E	F	I	G	H	P	F	T	A	I	L	V	A	C	L	V	A	I	Y	G	L	A	M	R	Q	G	M	P	K	D	K	V	M	E	I	C	G	H	A	L
Secondary structure
SS confidence
Disorder										?		?		?																															?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		Q	P	A	G	I	I	L	L	V	I	G	A	G	G	V	F	K	Q	V	L	V	D	S	G	V	G	P	A	L	G	E	A	L	T	G	M	G	L	P	I	A	I	T	C	F	V	L	A	A	A	V	R	I	I	Q	G	S	A	T	V
Secondary structure
SS confidence
Disorder																									?	?											?		?																	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		A	C	L	T	A	V	G	L	V	M	P	V	I	E	Q	L	N	Y	S	G	A	Q	M	A	A	L	S	I	C	I	A	G	G	S	I	V	V	S	H	V	N	D	A	G	F	W	L	F	G	K	F	T	G	A	T	E	A	E	T	L
Secondary structure
SS confidence
Disorder																	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.
Sequence		K	T	W	T	M	M	E	T	I	L	G	T	V	G	A	I	V	G	M	I	A	F	Q	L	L	S
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 2knc chain A Region: 171 - 222 Aligned: 52 Modelled: 52 Confidence: 12.1% Identity: 10% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1xd7 chain A Region: 371 - 423 Aligned: 53 Modelled: 53 Confidence: 7.0% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Transcriptional regulator Rrf2 Phyre2 PDB 2a65 chain A domain 1 Region: 94 - 291 Aligned: 184 Modelled: 198 Confidence: 5.2% Identity: 11% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 1 c2kncA_ 2 d1xd7a_ 3 d2a65a1

Detailed template information

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

1 c2kncA_ 12.1 10 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 d1xd7a_ 7.0 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator Rrf2 3 d2a65a1 5.2 11 Fold:SNF-like Superfamily:SNF-like Family:SNF-like

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