Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	P	S	Q	H	A	E	Q	F	Q	S	Q	L	A	N	Y	V	P	Q	F	T	P	E	F	W	P	V	W	L	I	I	A	G	V	L	L	V	G	M	W	L	V	L	G	L	H	A	L	L	R	A	R	G	V	K	K	S	A	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?										?		?																																			?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	H	G	E	K	I	Y	L	Y	S	K	A	V	R	L	W	H	W	S	N	A	L	L	F	V	L	L	L	A	S	G	L	I	N	H	F	A	M	V	G	A	T	A	V	K	S	L	V	A	V	H	E	V	C	G	F	L	L	L	A
Secondary structure
SS confidence
Disorder		?	?	?																																				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		C	W	L	G	F	V	L	I	N	A	V	G	D	N	G	H	H	Y	R	I	R	R	Q	G	W	L	E	R	A	A	K	Q	T	R	F	Y	L	F	G	I	M	Q	G	E	E	H	P	F	P	A	T	T	Q	S	K	F	N	P	L	Q
Secondary structure
SS confidence
Disorder																																													?	?		?			?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		Q	V	A	Y	V	G	V	M	Y	G	L	L	P	L	L	L	L	T	G	L	L	C	L	Y	P	Q	A	V	G	D	V	F	P	G	V	R	Y	W	L	L	Q	T	H	F	A	L	A	F	I	S	L	F	F	I	F	G	H	L	Y	L
Secondary structure
SS confidence
Disorder																												?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.
Sequence		C	T	T	G	R	T	P	H	E	T	F	K	S	M	V	D	G	Y	H	R	H
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: 61 - 260 Aligned: 183 Modelled: 187 Confidence: 100.0% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Formate dehydrogenase N, cytochrome (gamma) subunit Phyre2 PDB 1bcc chain C domain 3 Region: 79 - 241 Aligned: 147 Modelled: 151 Confidence: 97.8% Identity: 14% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1ppj chain C domain 2 Region: 79 - 241 Aligned: 147 Modelled: 147 Confidence: 97.8% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3cwb chain C Region: 79 - 240 Aligned: 146 Modelled: 146 Confidence: 97.8% Identity: 13% 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 1q90 chain B Region: 79 - 249 Aligned: 155 Modelled: 155 Confidence: 97.6% Identity: 14% 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 C domain 2 Region: 79 - 241 Aligned: 147 Modelled: 147 Confidence: 97.6% Identity: 12% 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: 79 - 240 Aligned: 146 Modelled: 146 Confidence: 97.5% Identity: 12% 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 2e74 chain A domain 1 Region: 79 - 241 Aligned: 149 Modelled: 151 Confidence: 97.5% 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 2qjk chain M Region: 79 - 241 Aligned: 147 Modelled: 147 Confidence: 97.5% Identity: 13% 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 1kqf chain B domain 2 Region: 31 - 62 Aligned: 32 Modelled: 32 Confidence: 46.6% Identity: 9% Fold: Single transmembrane helix Superfamily: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor Family: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor Phyre2 PDB 2knc chain A Region: 22 - 65 Aligned: 44 Modelled: 44 Confidence: 20.3% Identity: 11% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3mk7 chain F Region: 29 - 103 Aligned: 71 Modelled: 75 Confidence: 9.6% Identity: 17% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 1y5i chain C domain 1 Region: 40 - 235 Aligned: 153 Modelled: 155 Confidence: 8.1% Identity: 13% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 1ji8 chain A Region: 2 - 26 Aligned: 25 Modelled: 25 Confidence: 7.6% Identity: 32% Fold: DsrC, the gamma subunit of dissimilatory sulfite reductase Superfamily: DsrC, the gamma subunit of dissimilatory sulfite reductase Family: DsrC, the gamma subunit of dissimilatory sulfite reductase Phyre2 PDB 2kxa chain A Region: 248 - 259 Aligned: 12 Modelled: 12 Confidence: 7.3% Identity: 25% PDB header:viral protein, immune system Chain: A: PDB Molecule:haemagglutinin ha2 chain peptide; PDBTitle: the hemagglutinin fusion peptide (h1 subtype) at ph 7.4 Phyre2 PDB 1fft chain G Region: 29 - 89 Aligned: 59 Modelled: 61 Confidence: 7.1% Identity: 17% PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli Phyre2 1 d1kqfc_ 2 d1bccc3 3 d1ppjc2 4 c3cwbC_ 5 d1q90b_ 6 d3cx5c2 7 c3cx5N_ 8 d2e74a1 9 c2qjkM_ 10 d1kqfb2 11 c2kncA_ 12 c3mk7F_ 13 d1y5ic1 14 d1ji8a_ 15 c2kxaA_ 16 c1fftG_

Detailed template information

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

1 d1kqfc_ 100.0 17 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 2 d1bccc3 97.8 14 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 3 d1ppjc2 97.8 15 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 4 c3cwbC_ 97.8 13 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 5 d1q90b_ 97.6 14 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 6 d3cx5c2 97.6 12 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 7 c3cx5N_ 97.5 12 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. 8 d2e74a1 97.5 17 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 c2qjkM_ 97.5 13 PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin 10 d1kqfb2 46.6 9 Fold:Single transmembrane helix Superfamily:Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor Family:Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor 11 c2kncA_ 20.3 11 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 12 c3mk7F_ 9.6 17 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 13 d1y5ic1 8.1 13 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 14 d1ji8a_ 7.6 32 Fold:DsrC, the gamma subunit of dissimilatory sulfite reductase Superfamily:DsrC, the gamma subunit of dissimilatory sulfite reductase Family:DsrC, the gamma subunit of dissimilatory sulfite reductase 15 c2kxaA_ 7.3 25 PDB header:viral protein, immune system Chain: A: PDB Molecule:haemagglutinin ha2 chain peptide; PDBTitle: the hemagglutinin fusion peptide (h1 subtype) at ph 7.4 16 c1fftG_ 7.1 17 PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli

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