Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	H	S	T	D	H	S	G	A	S	H	G	S	V	K	T	Y	M	T	G	F	I	L	S	I	I	L	T	V	I	P	F	W	M	V	M	T	G	A	A	S	P	A	V	I	L	G	T	I	L	A	M	A	V	V	Q	V	L	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.
Sequence		H	L	V	C	F	L	H	M	N	T	K	S	D	E	G	W	N	M	T	A	F	V	F	T	V	L	I	I	A	I	L	V	V	G	S	I	W	I	M	W	N	L	N	Y	N	M	M	M	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 1dxz chain A Region: 20 - 44 Aligned: 25 Modelled: 25 Confidence: 14.0% Identity: 16% PDB header:transmembrane protein Chain: A: PDB Molecule:acetylcholine receptor protein, alpha chain; PDBTitle: m2 transmembrane segment of alpha-subunit of nicotinic2 acetylcholine receptor from torpedo californica, nmr, 203 structures Phyre2 PDB 3din chain F Region: 51 - 100 Aligned: 49 Modelled: 50 Confidence: 13.8% Identity: 18% PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 2r6g chain F domain 1 Region: 16 - 63 Aligned: 48 Modelled: 48 Confidence: 13.6% Identity: 8% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 1xl7 chain A domain 2 Region: 54 - 65 Aligned: 12 Modelled: 12 Confidence: 9.8% Identity: 17% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 2wwa chain C Region: 20 - 27 Aligned: 8 Modelled: 8 Confidence: 8.8% Identity: 63% PDB header:ribosome Chain: C: PDB Molecule:protein transport protein seb2; PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 1t1u chain A domain 2 Region: 54 - 65 Aligned: 12 Modelled: 12 Confidence: 8.7% Identity: 25% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 3j01 chain A Region: 43 - 100 Aligned: 57 Modelled: 58 Confidence: 8.4% Identity: 21% PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment Phyre2 PDB 1ndb chain A domain 2 Region: 54 - 65 Aligned: 12 Modelled: 12 Confidence: 8.0% Identity: 33% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 1nm8 chain A domain 2 Region: 54 - 65 Aligned: 12 Modelled: 12 Confidence: 7.0% Identity: 25% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 2y69 chain W Region: 72 - 109 Aligned: 35 Modelled: 38 Confidence: 6.9% Identity: 11% PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 3dl8 chain H Region: 43 - 100 Aligned: 58 Modelled: 58 Confidence: 6.3% Identity: 17% PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 1oed chain C Region: 20 - 104 Aligned: 80 Modelled: 85 Confidence: 5.9% Identity: 21% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 2ksr chain A Region: 20 - 60 Aligned: 41 Modelled: 41 Confidence: 5.7% Identity: 10% 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 3eam chain B Region: 20 - 100 Aligned: 81 Modelled: 81 Confidence: 5.4% Identity: 15% 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 1rkl chain A Region: 72 - 93 Aligned: 22 Modelled: 22 Confidence: 5.4% Identity: 32% Fold: Single transmembrane helix Superfamily: Oligosaccharyltransferase subunit ost4p Family: Oligosaccharyltransferase subunit ost4p Phyre2 1 c1dxzA_ 2 c3dinF_ 3 d2r6gf1 4 d1xl7a2 5 c2wwaC_ 6 d1t1ua2 7 c3j01A_ 8 d1ndba2 9 d1nm8a2 10 c2y69W_ 11 c3dl8H_ 12 d1oedc_ 13 c2ksrA_ 14 c3eamB_ 15 d1rkla_

Detailed template information

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

1 c1dxzA_ 14.0 16 PDB header:transmembrane protein Chain: A: PDB Molecule:acetylcholine receptor protein, alpha chain; PDBTitle: m2 transmembrane segment of alpha-subunit of nicotinic2 acetylcholine receptor from torpedo californica, nmr, 203 structures 2 c3dinF_ 13.8 18 PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase 3 d2r6gf1 13.6 8 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 4 d1xl7a2 9.8 17 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 5 c2wwaC_ 8.8 63 PDB header:ribosome Chain: C: PDB Molecule:protein transport protein seb2; PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome 6 d1t1ua2 8.7 25 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 7 c3j01A_ 8.4 21 PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment 8 d1ndba2 8.0 33 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 9 d1nm8a2 7.0 25 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 10 c2y69W_ 6.9 11 PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 11 c3dl8H_ 6.3 17 PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 12 d1oedc_ 5.9 21 Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore 13 c2ksrA_ 5.7 10 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 14 c3eamB_ 5.4 15 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 15 d1rkla_ 5.4 32 Fold:Single transmembrane helix Superfamily:Oligosaccharyltransferase subunit ost4p Family:Oligosaccharyltransferase subunit ost4p

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