Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	G	S	M	I	V	N	N	L	A	G	L	M	M	L	T	S	L	F	V	I	S	V	K	S	Y	R	L	S	C	G	F	Y	A	C	Q	S	L	V	L	V	S	I	F	A	T	L	S	C	L	F	A	A	E	Q	L	L	I	W
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	A	S	A	F	I	T	K	V	L	L	V	P	L	I	M	T	Y	A	A	R	N	I	P	Q	N	I	P	E	K	A	L	F	G	P	A	M	M	A	L	L	A	A	L	I	V	L	L	C	A	F	V	V	Q	P	V	K	L	P	M
Secondary structure
SS confidence
Disorder																																	?																							?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	T	G	L	K	P	A	L	A	V	A	L	G	H	F	L	L	G	L	L	C	I	V	S	Q	R	N	I	L	R	Q	I	F	G	Y	C	L	M	E	N	G	S	H	L	V	L	A	L	L	A	W	R	A	P	E	L	V	E	I	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.
Sequence		I	A	T	D	A	I	F	A	V	I	V	M	V	L	L	A	R	K	I	W	R	T	H	G	T	L	D	V	N	N	L	T	A	L	K	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 3rko chain K Region: 125 - 216 Aligned: 91 Modelled: 92 Confidence: 98.6% Identity: 23% 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 3rko chain N Region: 24 - 216 Aligned: 183 Modelled: 193 Confidence: 20.7% Identity: 14% PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain M Region: 88 - 214 Aligned: 125 Modelled: 127 Confidence: 20.2% Identity: 12% PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2jo1 chain A Region: 115 - 146 Aligned: 32 Modelled: 32 Confidence: 15.2% Identity: 28% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 2jp3 chain A Region: 115 - 146 Aligned: 32 Modelled: 32 Confidence: 13.2% Identity: 13% PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles Phyre2 PDB 1v8c chain A domain 2 Region: 73 - 90 Aligned: 18 Modelled: 18 Confidence: 5.6% Identity: 6% Fold: TBP-like Superfamily: MoaD-related protein, C-terminal domain Family: MoaD-related protein, C-terminal domain Phyre2 1 c3rkoK_ 2 c3rkoN_ 3 c3rkoM_ 4 c2jo1A_ 5 c2jp3A_ 6 d1v8ca2

Detailed template information

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

1 c3rkoK_ 98.6 23 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 2 c3rkoN_ 20.7 14 PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 3 c3rkoM_ 20.2 12 PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 4 c2jo1A_ 15.2 28 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 5 c2jp3A_ 13.2 13 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 6 d1v8ca2 5.6 6 Fold:TBP-like Superfamily:MoaD-related protein, C-terminal domain Family:MoaD-related protein, C-terminal domain

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