Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	Q	K	S	D	N	V	V	S	H	Y	V	F	E	A	P	V	R	I	W	H	W	L	T	V	L	C	M	A	V	L	M	V	T	G	Y	F	I	G	K	P	L	P	S	V	S	G	E	A	T	Y	L	F	Y	M	G	Y	I	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																																				?	?	?			?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	I	H	F	S	A	G	M	V	F	T	V	V	L	L	M	R	I	Y	W	A	F	V	G	N	R	Y	S	R	E	L	F	I	V	P	V	W	R	K	S	W	W	Q	G	V	W	Y	E	I	R	W	Y	L	F	L	A	K	R	P	S
Secondary structure
SS confidence
Disorder																																	?			?	?	?																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	D	I	G	H	N	P	I	A	Q	A	A	M	F	G	Y	F	L	M	S	V	F	M	I	I	T	G	F	A	L	Y	S	E	H	S	Q	Y	A	I	F	A	P	F	R	Y	V	V	E	F	F	Y	W	T	G	G	N	S	M	D	I
Secondary structure
SS confidence
Disorder																																			?	?	?	?	?											?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.
Sequence		H	S	W	H	R	L	G	M	W	L	I	G	A	F	V	I	G	H	V	Y	M	A	L	R	E	D	I	M	S	D	D	T	V	I	S	T	M	V	N	G	Y	R	S	H	K	F	G	K	I	S	N	K	E	R	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 1kqf chain C Region: 6 - 228 Aligned: 193 Modelled: 208 Confidence: 100.0% Identity: 16% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Formate dehydrogenase N, cytochrome (gamma) subunit Phyre2 PDB 2qjk chain M Region: 24 - 213 Aligned: 155 Modelled: 155 Confidence: 98.3% Identity: 15% PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin Phyre2 PDB 3cx5 chain C domain 2 Region: 24 - 213 Aligned: 155 Modelled: 155 Confidence: 98.3% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3cx5 chain N Region: 24 - 213 Aligned: 155 Modelled: 155 Confidence: 98.2% Identity: 17% PDB header:oxidoreductase Chain: N: PDB Molecule:cytochrome b; PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer. Phyre2 PDB 3cwb chain C Region: 24 - 213 Aligned: 153 Modelled: 154 Confidence: 98.2% Identity: 16% PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d Phyre2 PDB 1ppj chain C domain 2 Region: 24 - 213 Aligned: 153 Modelled: 154 Confidence: 98.1% Identity: 18% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1q90 chain B Region: 24 - 205 Aligned: 147 Modelled: 147 Confidence: 98.0% Identity: 18% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1bcc chain C domain 3 Region: 24 - 205 Aligned: 145 Modelled: 146 Confidence: 98.0% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 2e74 chain A domain 1 Region: 24 - 205 Aligned: 147 Modelled: 147 Confidence: 97.9% Identity: 18% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1y5i chain C domain 1 Region: 1 - 196 Aligned: 147 Modelled: 158 Confidence: 84.7% Identity: 7% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 3eh4 chain A Region: 6 - 148 Aligned: 111 Modelled: 111 Confidence: 53.0% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus Phyre2 PDB 2axt chain A domain 1 Region: 123 - 228 Aligned: 105 Modelled: 106 Confidence: 16.0% Identity: 14% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 1 d1kqfc_ 2 c2qjkM_ 3 d3cx5c2 4 c3cx5N_ 5 c3cwbC_ 6 d1ppjc2 7 d1q90b_ 8 d1bccc3 9 d2e74a1 10 d1y5ic1 11 c3eh4A_ 12 d2axta1

Detailed template information

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

1 d1kqfc_ 100.0 16 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 2 c2qjkM_ 98.3 15 PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin 3 d3cx5c2 98.3 17 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 4 c3cx5N_ 98.2 17 PDB header:oxidoreductase Chain: N: PDB Molecule:cytochrome b; PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer. 5 c3cwbC_ 98.2 16 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 6 d1ppjc2 98.1 18 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 7 d1q90b_ 98.0 18 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 8 d1bccc3 98.0 17 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 d2e74a1 97.9 18 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 10 d1y5ic1 84.7 7 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 11 c3eh4A_ 53.0 14 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus 12 d2axta1 16.0 14 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits

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