Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	D	Y	E	V	L	R	F	I	W	W	L	L	V	G	V	L	L	I	G	F	A	V	T	D	G	F	D	M	G	V	G	M	L	T	R	F	L	G	R	N	D	T	E	R	R	I	M	I	N	S	I	A	P	H	W	D	G	N
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	V	W	L	I	T	A	G	G	A	L	F	A	A	W	P	M	V	Y	A	A	A	F	S	G	F	Y	V	A	M	I	L	V	L	A	S	L	F	F	R	P	V	G	F	D	Y	R	S	K	I	E	E	T	R	W	R	N	M	W	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		W	G	I	F	I	G	S	F	V	P	P	L	V	I	G	V	A	F	G	N	L	L	Q	G	V	P	F	N	V	D	E	Y	L	R	L	Y	Y	T	G	N	F	F	Q	L	L	N	P	F	G	L	L	A	G	V	V	S	V	G	M	I
Secondary structure
SS confidence
Disorder																													?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	T	Q	G	A	T	Y	L	Q	M	R	T	V	G	E	L	H	L	R	T	R	A	T	A	Q	V	A	A	L	V	T	L	V	C	F	A	L	A	G	V	W	V	M	Y	G	I	D	G	Y	V	V	K	S	T	M	D	H	Y	A	A
Secondary structure
SS confidence
Disorder																																																?		?	?	?	?	?		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	N	P	L	N	K	E	V	V	R	E	A	G	A	W	L	V	N	F	N	N	T	P	I	L	W	A	I	P	A	L	G	V	V	L	P	L	L	T	I	L	T	A	R	M	D	K	A	A	W	A	F	V	F	S	S	L	T	L	A
Secondary structure
SS confidence
Disorder		?		?	?	?	?	?	?		?		?																																?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		C	I	I	L	T	A	G	I	A	M	F	P	F	V	M	P	S	S	T	M	M	N	A	S	L	T	M	W	D	A	T	S	S	Q	L	T	L	N	V	M	T	W	V	A	V	V	L	V	P	I	I	L	L	Y	T	A	W	C	Y	W
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.
Sequence		K	M	F	G	R	I	T	K	E	D	I	E	R	N	T	H	S	L	Y
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 1fft chain B domain 2 Region: 317 - 378 Aligned: 59 Modelled: 62 Confidence: 20.9% Identity: 14% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1ar1 chain B Region: 319 - 377 Aligned: 59 Modelled: 59 Confidence: 16.5% Identity: 10% PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment Phyre2 PDB 1qle chain B Region: 318 - 376 Aligned: 59 Modelled: 59 Confidence: 15.8% Identity: 10% PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment Phyre2 PDB 1ejx chain C domain 2 Region: 308 - 339 Aligned: 32 Modelled: 32 Confidence: 11.7% Identity: 25% Fold: TIM beta/alpha-barrel Superfamily: Metallo-dependent hydrolases Family: alpha-subunit of urease, catalytic domain Phyre2 PDB 1e9y chain B domain 2 Region: 308 - 339 Aligned: 32 Modelled: 32 Confidence: 11.0% Identity: 22% Fold: TIM beta/alpha-barrel Superfamily: Metallo-dependent hydrolases Family: alpha-subunit of urease, catalytic domain Phyre2 PDB 3m7b chain A Region: 129 - 371 Aligned: 188 Modelled: 197 Confidence: 10.8% Identity: 12% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:tellurite resistance protein teha homolog; PDBTitle: crystal structure of plant slac1 homolog teha Phyre2 PDB 2kta chain A Region: 40 - 58 Aligned: 19 Modelled: 19 Confidence: 6.8% Identity: 26% PDB header:hydrolase Chain: A: PDB Molecule:putative helicase; PDBTitle: solution nmr structure of a domain of protein a6ky75 from bacteroides2 vulgatus, northeast structural genomics target bvr106a Phyre2 PDB 2knc chain A Region: 339 - 376 Aligned: 38 Modelled: 38 Confidence: 6.2% Identity: 16% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2f3o chain B Region: 42 - 62 Aligned: 21 Modelled: 21 Confidence: 5.6% Identity: 19% PDB header:unknown function Chain: B: PDB Molecule:pyruvate formate-lyase 2; PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus Phyre2 1 d1fftb2 2 c1ar1B_ 3 c1qleB_ 4 d1ejxc2 5 d1e9yb2 6 c3m7bA_ 7 c2ktaA_ 8 c2kncA_ 9 c2f3oB_

Detailed template information

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

1 d1fftb2 20.9 14 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 2 c1ar1B_ 16.5 10 PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment 3 c1qleB_ 15.8 10 PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment 4 d1ejxc2 11.7 25 Fold:TIM beta/alpha-barrel Superfamily:Metallo-dependent hydrolases Family:alpha-subunit of urease, catalytic domain 5 d1e9yb2 11.0 22 Fold:TIM beta/alpha-barrel Superfamily:Metallo-dependent hydrolases Family:alpha-subunit of urease, catalytic domain 6 c3m7bA_ 10.8 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:tellurite resistance protein teha homolog; PDBTitle: crystal structure of plant slac1 homolog teha 7 c2ktaA_ 6.8 26 PDB header:hydrolase Chain: A: PDB Molecule:putative helicase; PDBTitle: solution nmr structure of a domain of protein a6ky75 from bacteroides2 vulgatus, northeast structural genomics target bvr106a 8 c2kncA_ 6.2 16 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 9 c2f3oB_ 5.6 19 PDB header:unknown function Chain: B: PDB Molecule:pyruvate formate-lyase 2; PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus

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