Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	R	D	T	I	V	R	Y	T	A	P	E	R	I	N	H	W	I	T	A	F	C	F	I	L	A	A	V	S	G	L	G	F	L	F	P	S	F	N	W	L	M	Q	I	M	G	T	P	Q	L	A	R	I	L	H	P	F	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	V	V	M	F	A	S	F	I	I	M	F	F	R	Y	W	H	H	N	L	I	N	R	D	D	I	F	W	A	K	N	I	R	K	I	V	V	N	E	E	V	G	D	T	G	R	Y	N	F	G	Q	K	C	V	F	W	A	A	I	I
Secondary structure
SS confidence
Disorder																			?																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	L	V	L	L	L	V	S	G	V	I	I	W	R	P	Y	F	A	P	A	F	S	I	P	V	I	R	F	A	L	M	L	H	S	F	A	A	V	A	L	I	V	V	I	M	V	H	I	Y	A	A	L	W	V	K	G	T	I	T	A
Secondary structure
SS confidence
Disorder																		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.
Sequence		M	V	E	G	W	V	T	S	A	W	A	K	K	H	H	P	R	W	Y	R	E	V	R	K	T	T	E	K	K	A	E
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: 2 - 210 Aligned: 209 Modelled: 209 Confidence: 100.0% Identity: 48% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Formate dehydrogenase N, cytochrome (gamma) subunit Phyre2 PDB 2qjk chain M Region: 20 - 171 Aligned: 152 Modelled: 152 Confidence: 98.2% Identity: 17% 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 1q90 chain B Region: 20 - 171 Aligned: 152 Modelled: 152 Confidence: 98.1% Identity: 19% 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: 20 - 171 Aligned: 152 Modelled: 152 Confidence: 98.1% 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 N Region: 20 - 171 Aligned: 152 Modelled: 152 Confidence: 98.1% Identity: 14% 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: 20 - 171 Aligned: 151 Modelled: 152 Confidence: 98.1% Identity: 14% 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 1bcc chain C domain 3 Region: 20 - 171 Aligned: 151 Modelled: 152 Confidence: 98.0% 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: 20 - 171 Aligned: 151 Modelled: 152 Confidence: 98.0% Identity: 13% 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: 20 - 171 Aligned: 152 Modelled: 152 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 1y5i chain C domain 1 Region: 16 - 165 Aligned: 115 Modelled: 124 Confidence: 42.5% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 3mk7 chain K Region: 1 - 191 Aligned: 168 Modelled: 169 Confidence: 33.4% Identity: 14% PDB header:oxidoreductase Chain: K: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit n; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 2kyg chain C Region: 183 - 205 Aligned: 22 Modelled: 23 Confidence: 33.3% Identity: 27% PDB header:protein binding Chain: C: PDB Molecule:protein cbfa2t1; PDBTitle: structure of the aml1-eto nervy domain - pka(riia) complex and its2 contribution to aml1-eto activity Phyre2 PDB 2lev chain A Region: 196 - 211 Aligned: 16 Modelled: 16 Confidence: 31.3% Identity: 38% PDB header:transcription regulator/dna Chain: A: PDB Molecule:ler; PDBTitle: structure of the dna complex of the c-terminal domain of ler Phyre2 PDB 3kmp chain A Region: 184 - 211 Aligned: 28 Modelled: 28 Confidence: 14.0% Identity: 21% PDB header:transcription regulator/dna Chain: A: PDB Molecule:smad1-mh1; PDBTitle: crystal structure of smad1-mh1/dna complex Phyre2 PDB 1m56 chain D Region: 1 - 34 Aligned: 34 Modelled: 34 Confidence: 13.4% Identity: 12% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1hnr chain A Region: 196 - 211 Aligned: 16 Modelled: 16 Confidence: 9.7% Identity: 6% Fold: H-NS histone-like proteins Superfamily: H-NS histone-like proteins Family: H-NS histone-like proteins Phyre2 PDB 2od6 chain A domain 1 Region: 188 - 206 Aligned: 19 Modelled: 19 Confidence: 7.0% Identity: 21% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: Marine metagenome family DABB1 Phyre2 PDB 2l4g chain A Region: 168 - 188 Aligned: 21 Modelled: 17 Confidence: 6.0% Identity: 14% PDB header:viral protein Chain: A: PDB Molecule:haemagglutinin; PDBTitle: influenza haemagglutinin fusion peptide mutant g13a Phyre2 PDB 1fcu chain A Region: 187 - 210 Aligned: 24 Modelled: 24 Confidence: 6.0% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase Phyre2 PDB 1rrz chain A Region: 182 - 201 Aligned: 15 Modelled: 20 Confidence: 5.9% Identity: 27% Fold: Spectrin repeat-like Superfamily: Glycogen synthesis protein GlgS Family: Glycogen synthesis protein GlgS Phyre2 1 d1kqfc_ 2 c2qjkM_ 3 d1q90b_ 4 d3cx5c2 5 c3cx5N_ 6 c3cwbC_ 7 d1bccc3 8 d1ppjc2 9 d2e74a1 10 d1y5ic1 11 c3mk7K_ 12 c2kygC_ 13 c2levA_ 14 c3kmpA_ 15 d1m56d_ 16 d1hnra_ 17 d2od6a1 18 c2l4gA_ 19 c1fcuA_ 20 d1rrza_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 d1kqfc_ 100.0 48 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 2 c2qjkM_ 98.2 17 PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin 3 d1q90b_ 98.1 19 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 4 d3cx5c2 98.1 14 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 5 c3cx5N_ 98.1 14 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. 6 c3cwbC_ 98.1 14 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 7 d1bccc3 98.0 14 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 8 d1ppjc2 98.0 13 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 9 d2e74a1 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) 10 d1y5ic1 42.5 17 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 11 c3mk7K_ 33.4 14 PDB header:oxidoreductase Chain: K: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit n; PDBTitle: the structure of cbb3 cytochrome oxidase 12 c2kygC_ 33.3 27 PDB header:protein binding Chain: C: PDB Molecule:protein cbfa2t1; PDBTitle: structure of the aml1-eto nervy domain - pka(riia) complex and its2 contribution to aml1-eto activity 13 c2levA_ 31.3 38 PDB header:transcription regulator/dna Chain: A: PDB Molecule:ler; PDBTitle: structure of the dna complex of the c-terminal domain of ler 14 c3kmpA_ 14.0 21 PDB header:transcription regulator/dna Chain: A: PDB Molecule:smad1-mh1; PDBTitle: crystal structure of smad1-mh1/dna complex 15 d1m56d_ 13.4 12 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 16 d1hnra_ 9.7 6 Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins 17 d2od6a1 7.0 21 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Marine metagenome family DABB1 18 c2l4gA_ 6.0 14 PDB header:viral protein Chain: A: PDB Molecule:haemagglutinin; PDBTitle: influenza haemagglutinin fusion peptide mutant g13a 19 c1fcuA_ 6.0 17 PDB header:hydrolase Chain: A: PDB Molecule:hyaluronoglucosaminidase; PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase 20 d1rrza_ 5.9 27 Fold:Spectrin repeat-like Superfamily:Glycogen synthesis protein GlgS Family:Glycogen synthesis protein GlgS 21 c1rrzA_ not modelled 5.9 27 PDB header:structural genomics,biosynthetic protein Chain: A: PDB Molecule:glycogen synthesis protein glgs; PDBTitle: solution structure of glgs protein from e. coli 22 d1v0da_ not modelled 5.8 15 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:Caspase-activated DNase, CAD (DffB, DFF40) 23 c1v0dA_ not modelled 5.8 15 PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad) 24 d1fcqa_ not modelled 5.4 17 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Bee venom hyaluronidase 25 c3nrtC_ not modelled 5.3 14 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:putative ryanodine receptor; PDBTitle: the crystal strucutre of putative ryanodine receptor from bacteroides2 thetaiotaomicron vpi-5482 26 c1m46B_ not modelled 5.2 17 PDB header:cell cycle protein Chain: B: PDB Molecule:iq4 motif from myo2p, a class v myosin; PDBTitle: crystal structure of mlc1p bound to iq4 of myo2p, a class v2 myosin 27 d1ecfa1 not modelled 5.1 10 Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases) 28 c1xooA_ not modelled 5.0 15 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1s mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5

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