Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	M	L	A	L	T	I	I	L	P	L	I	G	F	V	L	L	A	F	S	R	G	R	W	S	E	N	V	S	A	I	V	G	V	G	S	V	G	L	A	A	L	V	T	A	F	I	G	V	D	F	F	A	N	G	E	Q	T	Y
Secondary structure
SS confidence
Disorder		?	?																			?	?	?	?																														?			?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	Q	P	L	W	T	W	M	S	V	G	D	F	N	I	G	F	N	L	V	L	D	G	L	S	L	T	M	L	S	V	V	T	G	V	G	F	L	I	H	M	Y	A	S	W	Y	M	R	G	E	E	G	Y	S	R	F	F	A	Y	T
Secondary structure
SS confidence
Disorder							?			?		?	?																																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	L	F	I	A	S	M	V	V	L	V	L	A	D	N	L	L	L	M	Y	L	G	W	E	G	V	G	L	C	S	Y	L	L	I	G	F	Y	Y	T	D	P	K	N	G	A	A	A	M	K	A	F	V	V	T	R	V	G	D	V	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	A	F	A	L	F	I	L	Y	N	E	L	G	T	L	N	F	R	E	M	V	E	L	A	P	A	H	F	A	D	G	N	N	M	L	M	W	A	T	L	M	L	L	G	G	A	V	G	K	S	A	Q	L	P	L	Q	T	W	L	A
Secondary structure
SS confidence
Disorder																							?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		D	A	M	A	G	P	T	P	V	S	A	L	I	H	A	A	T	M	V	T	A	G	V	Y	L	I	A	R	T	H	G	L	F	L	M	T	P	E	V	L	H	L	V	G	I	V	G	A	V	T	L	L	L	A	G	F	A	A	L	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		Q	T	D	I	K	R	V	L	A	Y	S	T	M	S	Q	I	G	Y	M	F	L	A	L	G	V	Q	A	W	D	A	A	I	F	H	L	M	T	H	A	F	F	K	A	L	L	F	L	A	S	G	S	V	I	L	A	C	H	H	E	Q
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		N	I	F	K	M	G	G	L	R	K	S	I	P	L	V	Y	L	C	F	L	V	G	G	A	A	L	S	A	L	P	L	V	T	A	G	F	F	S	K	D	E	I	L	A	G	A	M	A	N	G	H	I	N	L	M	V	A	G	L	V
Secondary structure
SS confidence
Disorder							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		G	A	F	M	T	S	L	Y	T	F	R	M	I	F	I	V	F	H	G	K	E	Q	I	H	A	H	A	V	K	G	V	T	H	S	L	P	L	I	V	L	L	I	L	S	T	F	V	G	A	L	I	V	P	P	L	Q	G	V	L	P
Secondary structure
SS confidence
Disorder																				?		?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		Q	T	T	E	L	A	H	G	S	M	L	T	L	E	I	T	S	G	V	V	A	V	V	G	I	L	L	A	A	W	L	W	L	G	K	R	T	L	V	T	S	I	A	N	S	A	P	G	R	L	L	G	T	W	W	Y	N	A	W	G
Secondary structure
SS confidence
Disorder					?	?																													?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600
Sequence		F	D	W	L	Y	D	K	V	F	V	K	P	F	L	G	I	A	W	L	L	K	R	D	P	L	N	S	M	M	N	I	P	A	V	L	S	R	F	A	G	K	G	L	L	L	S	E	N	G	Y	L	R	W	Y	V	A	S	M	S	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	610	.	.	.
Sequence		G	A	V	V	V	L	A	L	L	M	V	L	R
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 L Region: 1 - 612 Aligned: 612 Modelled: 612 Confidence: 100.0% Identity: 100% PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; 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: 3 - 487 Aligned: 479 Modelled: 484 Confidence: 100.0% Identity: 20% 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 3rko chain N Region: 1 - 483 Aligned: 459 Modelled: 467 Confidence: 100.0% Identity: 19% 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 K Region: 116 - 200 Aligned: 85 Modelled: 85 Confidence: 83.0% Identity: 22% 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 1a6q chain A domain 1 Region: 374 - 409 Aligned: 35 Modelled: 36 Confidence: 27.5% Identity: 17% Fold: Another 3-helical bundle Superfamily: Protein serine/threonine phosphatase 2C, C-terminal domain Family: Protein serine/threonine phosphatase 2C, C-terminal domain Phyre2 PDB 2l3i chain A Region: 298 - 309 Aligned: 12 Modelled: 12 Confidence: 18.5% Identity: 50% PDB header:antimicrobial protein Chain: A: PDB Molecule:aoxki4a, antimicrobial peptide in spider venom; PDBTitle: oxki4a, spider derived antimicrobial peptide Phyre2 PDB 1o8b chain B domain 1 Region: 301 - 337 Aligned: 34 Modelled: 37 Confidence: 17.9% Identity: 15% Fold: NagB/RpiA/CoA transferase-like Superfamily: NagB/RpiA/CoA transferase-like Family: D-ribose-5-phosphate isomerase (RpiA), catalytic domain Phyre2 PDB 1s1q chain A Region: 233 - 248 Aligned: 16 Modelled: 16 Confidence: 11.8% Identity: 31% Fold: UBC-like Superfamily: UBC-like Family: UEV domain Phyre2 PDB 1bcc chain E domain 2 Region: 108 - 141 Aligned: 34 Modelled: 34 Confidence: 6.8% Identity: 18% Fold: Single transmembrane helix Superfamily: ISP transmembrane anchor Family: ISP transmembrane anchor Phyre2 PDB 3d37 chain A domain 2 Region: 237 - 244 Aligned: 8 Modelled: 8 Confidence: 6.1% Identity: 38% Fold: Phage tail proteins Superfamily: Phage tail proteins Family: Baseplate protein-like Phyre2 1 c3rkoL_ 2 c3rkoM_ 3 c3rkoN_ 4 c3rkoK_ 5 d1a6qa1 6 c2l3iA_ 7 d1o8bb1 8 d1s1qa_ 9 d1bcce2 10 d3d37a2

Detailed template information

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

1 c3rkoL_ 100.0 100 PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 2 c3rkoM_ 100.0 20 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 3 c3rkoN_ 100.0 19 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 4 c3rkoK_ 83.0 22 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 5 d1a6qa1 27.5 17 Fold:Another 3-helical bundle Superfamily:Protein serine/threonine phosphatase 2C, C-terminal domain Family:Protein serine/threonine phosphatase 2C, C-terminal domain 6 c2l3iA_ 18.5 50 PDB header:antimicrobial protein Chain: A: PDB Molecule:aoxki4a, antimicrobial peptide in spider venom; PDBTitle: oxki4a, spider derived antimicrobial peptide 7 d1o8bb1 17.9 15 Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain 8 d1s1qa_ 11.8 31 Fold:UBC-like Superfamily:UBC-like Family:UEV domain 9 d1bcce2 6.8 18 Fold:Single transmembrane helix Superfamily:ISP transmembrane anchor Family:ISP transmembrane anchor 10 d3d37a2 6.1 38 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:Baseplate protein-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