Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	N	K	I	S	T	Y	S	P	A	F	S	I	V	S	W	I	A	L	V	G	G	I	V	T	Y	L	L	G	L	W	N	A	E	M	Q	L	N	E	K	G	Y	Y	F	A	V	L	V	L	G	L	F	S	A	A	S	Y	Q	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?																										?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	V	R	D	K	Y	E	G	I	P	T	T	S	I	Y	Y	M	T	C	L	T	V	F	I	I	S	V	A	L	L	M	V	G	L	W	N	A	T	L	L	L	S	E	K	G	F	Y	G	L	A	F	F	L	S	L	F	G	A	V	A
Secondary structure
SS confidence
Disorder								?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.
Sequence		V	Q	K	N	I	R	D	A	G	I	N	P	P	K	E	T	Q	V	T	Q	E	E	Y	S	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 2bg9 chain B Region: 4 - 137 Aligned: 118 Modelled: 119 Confidence: 63.4% Identity: 14% PDB header:ion channel/receptor Chain: B: PDB Molecule:acetylcholine receptor protein, beta chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. Phyre2 PDB 2knc chain B Region: 105 - 145 Aligned: 39 Modelled: 41 Confidence: 60.6% Identity: 10% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1vpu chain A Region: 121 - 145 Aligned: 25 Modelled: 25 Confidence: 51.4% Identity: 24% Fold: HIV-1 VPU cytoplasmic domain Superfamily: HIV-1 VPU cytoplasmic domain Family: HIV-1 VPU cytoplasmic domain Phyre2 PDB 3ria chain C Region: 4 - 95 Aligned: 92 Modelled: 92 Confidence: 44.1% Identity: 7% PDB header:transport protein/immune system Chain: C: PDB Molecule:avermectin-sensitive glutamate-gated chloride channel glucl PDBTitle: c. elegans glutamate-gated chloride channel (glucl) in complex with2 fab, ivermectin and iodide. Phyre2 PDB 1kqf chain C Region: 2 - 119 Aligned: 118 Modelled: 118 Confidence: 43.1% Identity: 14% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Formate dehydrogenase N, cytochrome (gamma) subunit Phyre2 PDB 2bg9 chain A Region: 4 - 92 Aligned: 88 Modelled: 89 Confidence: 32.4% Identity: 14% PDB header:ion channel/receptor Chain: A: PDB Molecule:acetylcholine receptor protein, alpha chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. Phyre2 PDB 2bg9 chain C Region: 4 - 142 Aligned: 123 Modelled: 124 Confidence: 30.7% Identity: 11% PDB header:ion channel/receptor Chain: C: PDB Molecule:acetylcholine receptor protein, delta chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. Phyre2 PDB 3eam chain B Region: 4 - 95 Aligned: 90 Modelled: 92 Confidence: 26.6% Identity: 9% PDB header:membrane protein, transport protein Chain: B: PDB Molecule:glr4197 protein; PDBTitle: an open-pore structure of a bacterial pentameric ligand-2 gated ion channel Phyre2 PDB 1m8o chain B Region: 121 - 145 Aligned: 25 Modelled: 25 Confidence: 23.4% Identity: 12% PDB header:membrane protein Chain: B: PDB Molecule:platele integrin beta3 subunit: cytoplasmic PDBTitle: platelet integrin alfaiib-beta3 cytoplasmic domain Phyre2 PDB 1s4x chain A Region: 121 - 145 Aligned: 25 Modelled: 25 Confidence: 22.3% Identity: 12% PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: nmr structure of the integrin b3 cytoplasmic domain in dpc2 micelles Phyre2 PDB 2ksr chain A Region: 6 - 92 Aligned: 86 Modelled: 87 Confidence: 18.7% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of tm domain of the n-acetylcholine receptor b2 subunit Phyre2 PDB 3g9w chain C Region: 124 - 145 Aligned: 22 Modelled: 22 Confidence: 14.6% Identity: 14% PDB header:cell adhesion Chain: C: PDB Molecule:integrin beta-1d; PDBTitle: crystal structure of talin2 f2-f3 in complex with the integrin beta1d2 cytoplasmic tail Phyre2 PDB 1q90 chain L Region: 13 - 32 Aligned: 20 Modelled: 20 Confidence: 11.1% Identity: 30% PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii Phyre2 PDB 1q90 chain L Region: 13 - 32 Aligned: 20 Modelled: 20 Confidence: 11.1% Identity: 30% Fold: Single transmembrane helix Superfamily: PetL subunit of the cytochrome b6f complex Family: PetL subunit of the cytochrome b6f complex Phyre2 PDB 1j46 chain A Region: 1 - 16 Aligned: 16 Modelled: 16 Confidence: 9.6% Identity: 25% Fold: HMG-box Superfamily: HMG-box Family: HMG-box Phyre2 PDB 1kuz chain B Region: 124 - 144 Aligned: 21 Modelled: 21 Confidence: 9.2% Identity: 14% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: solution structure of the membrane proximal regions of2 alpha-iib and beta-3 integrins Phyre2 PDB 1uaz chain A Region: 4 - 137 Aligned: 134 Modelled: 134 Confidence: 8.1% Identity: 13% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 2bg9 chain E Region: 4 - 137 Aligned: 126 Modelled: 126 Confidence: 7.9% Identity: 10% PDB header:ion channel/receptor Chain: E: PDB Molecule:acetylcholine receptor protein, gamma chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. Phyre2 PDB 3omy chain B Region: 61 - 97 Aligned: 31 Modelled: 37 Confidence: 6.6% Identity: 19% PDB header:dna binding protein Chain: B: PDB Molecule:protein tram; PDBTitle: crystal structure of the ped208 tram n-terminal domain Phyre2 PDB 1i7n chain A domain 1 Region: 122 - 145 Aligned: 24 Modelled: 24 Confidence: 6.1% Identity: 33% Fold: PreATP-grasp domain Superfamily: PreATP-grasp domain Family: Synapsin domain Phyre2 1 c2bg9B_ 2 c2kncB_ 3 d1vpua_ 4 c3riaC_ 5 d1kqfc_ 6 c2bg9A_ 7 c2bg9C_ 8 c3eamB_ 9 c1m8oB_ 10 c1s4xA_ 11 c2ksrA_ 12 c3g9wC_ 13 c1q90L_ 14 d1q90l_ 15 d1j46a_ 16 c1kuzB_ 17 d1uaza_ 18 c2bg9E_ 19 c3omyB_ 20 d1i7na1 21 22 23 24

Detailed template information

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

1 c2bg9B_ 63.4 14 PDB header:ion channel/receptor Chain: B: PDB Molecule:acetylcholine receptor protein, beta chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. 2 c2kncB_ 60.6 10 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 3 d1vpua_ 51.4 24 Fold:HIV-1 VPU cytoplasmic domain Superfamily:HIV-1 VPU cytoplasmic domain Family:HIV-1 VPU cytoplasmic domain 4 c3riaC_ 44.1 7 PDB header:transport protein/immune system Chain: C: PDB Molecule:avermectin-sensitive glutamate-gated chloride channel glucl PDBTitle: c. elegans glutamate-gated chloride channel (glucl) in complex with2 fab, ivermectin and iodide. 5 d1kqfc_ 43.1 14 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 6 c2bg9A_ 32.4 14 PDB header:ion channel/receptor Chain: A: PDB Molecule:acetylcholine receptor protein, alpha chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. 7 c2bg9C_ 30.7 11 PDB header:ion channel/receptor Chain: C: PDB Molecule:acetylcholine receptor protein, delta chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. 8 c3eamB_ 26.6 9 PDB header:membrane protein, transport protein Chain: B: PDB Molecule:glr4197 protein; PDBTitle: an open-pore structure of a bacterial pentameric ligand-2 gated ion channel 9 c1m8oB_ 23.4 12 PDB header:membrane protein Chain: B: PDB Molecule:platele integrin beta3 subunit: cytoplasmic PDBTitle: platelet integrin alfaiib-beta3 cytoplasmic domain 10 c1s4xA_ 22.3 12 PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: nmr structure of the integrin b3 cytoplasmic domain in dpc2 micelles 11 c2ksrA_ 18.7 16 PDB header:membrane protein Chain: A: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of tm domain of the n-acetylcholine receptor b2 subunit 12 c3g9wC_ 14.6 14 PDB header:cell adhesion Chain: C: PDB Molecule:integrin beta-1d; PDBTitle: crystal structure of talin2 f2-f3 in complex with the integrin beta1d2 cytoplasmic tail 13 c1q90L_ 11.1 30 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 14 d1q90l_ 11.1 30 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 15 d1j46a_ 9.6 25 Fold:HMG-box Superfamily:HMG-box Family:HMG-box 16 c1kuzB_ 9.2 14 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: solution structure of the membrane proximal regions of2 alpha-iib and beta-3 integrins 17 d1uaza_ 8.1 13 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 18 c2bg9E_ 7.9 10 PDB header:ion channel/receptor Chain: E: PDB Molecule:acetylcholine receptor protein, gamma chain; PDBTitle: refined structure of the nicotinic acetylcholine receptor2 at 4a resolution. 19 c3omyB_ 6.6 19 PDB header:dna binding protein Chain: B: PDB Molecule:protein tram; PDBTitle: crystal structure of the ped208 tram n-terminal domain 20 d1i7na1 6.1 33 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:Synapsin domain 21 c2etjA_ not modelled 6.1 26 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease hii; PDBTitle: crystal structure of ribonuclease hii (ec 3.1.26.4) (rnase hii)2 (tm0915) from thermotoga maritima at 1.74 a resolution 22 d2etja1 not modelled 6.1 26 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Ribonuclease H 23 d1qlec_ not modelled 5.9 18 Fold:Cytochrome c oxidase subunit III-like Superfamily:Cytochrome c oxidase subunit III-like Family:Cytochrome c oxidase subunit III-like 24 d1pk8a1 not modelled 5.9 25 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:Synapsin 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