Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	P	F	G	V	L	D	R	Y	I	G	K	T	I	F	T	T	I	M	M	T	L	F	M	L	V	S	L	S	G	I	I	K	F	V	D	Q	L	K	K	A	G	Q	G	S	Y	D	A	L	G	A	G	M	Y	T	L	L	S	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	K	D	V	Q	I	F	F	P	M	A	A	L	L	G	A	L	L	G	L	G	M	L	A	Q	R	S	E	L	V	V	M	Q	A	S	G	F	T	R	M	Q	V	A	L	S	V	M	K	T	A	I	P	L	V	L	L	T	M	A	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	E	W	V	A	P	Q	G	E	Q	M	A	R	N	Y	R	A	Q	A	M	Y	G	G	S	L	L	S	T	Q	Q	G	L	W	A	K	D	G	N	N	F	V	Y	I	E	R	V	K	G	D	E	E	L	G	G	I	S	I	Y	A	F
Secondary structure
SS confidence
Disorder																						?	?	?	?	?	?	?	?	?	?																		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		N	E	N	R	R	L	Q	S	V	R	Y	A	A	T	A	K	F	D	P	E	H	K	V	W	R	L	S	Q	V	D	E	S	D	L	T	N	P	K	Q	I	T	G	S	Q	T	V	S	G	T	W	K	T	N	L	T	P	D	K	L	G
Secondary structure
SS confidence
Disorder			?											?							?	?																?	?	?	?						?	?	?	?					?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	V	A	L	D	P	D	A	L	S	I	S	G	L	H	N	Y	V	K	Y	L	K	S	S	G	Q	D	A	G	R	Y	Q	L	N	M	W	S	K	I	F	Q	P	L	S	V	A	V	M	M	L	M	A	L	S	F	I	F	G	P	L
Secondary structure
SS confidence
Disorder			?	?	?		?	?	?												?	?	?	?	?	?	?	?	?																												?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		R	S	V	P	M	G	V	R	V	V	T	G	I	S	F	G	F	V	F	Y	V	L	D	Q	I	F	G	P	L	T	L	V	Y	G	I	P	P	I	I	G	A	L	L	P	S	A	S	F	F	L	I	S	L	W	L	L	M	R	K	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																																				?	?	?	?
Disorder confidence
Sequence
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 3my2 chain A Region: 163 - 235 Aligned: 73 Modelled: 73 Confidence: 50.9% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:lipopolysaccharide export system protein lptc; PDBTitle: crystal structure of lptc Phyre2 PDB 2rdc chain A Region: 4 - 15 Aligned: 12 Modelled: 12 Confidence: 14.4% Identity: 42% PDB header:lipid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution Phyre2 PDB 1utc chain A domain 2 Region: 156 - 234 Aligned: 77 Modelled: 79 Confidence: 12.6% Identity: 17% Fold: 7-bladed beta-propeller Superfamily: Clathrin heavy-chain terminal domain Family: Clathrin heavy-chain terminal domain Phyre2 PDB 1oed chain A Region: 10 - 127 Aligned: 118 Modelled: 118 Confidence: 10.3% Identity: 7% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 2voy chain H Region: 48 - 90 Aligned: 43 Modelled: 43 Confidence: 8.8% Identity: 14% PDB header:hydrolase Chain: H: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 1c9l chain A Region: 156 - 228 Aligned: 71 Modelled: 73 Confidence: 8.6% Identity: 15% PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:clathrin; PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin Phyre2 PDB 1bpo chain A Region: 156 - 234 Aligned: 77 Modelled: 79 Confidence: 8.5% Identity: 17% PDB header:membrane protein Chain: A: PDB Molecule:protein (clathrin); PDBTitle: clathrin heavy-chain terminal domain and linker Phyre2 PDB 1f5q chain B domain 1 Region: 5 - 35 Aligned: 31 Modelled: 31 Confidence: 8.0% Identity: 19% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 1j1u chain A Region: 65 - 136 Aligned: 67 Modelled: 72 Confidence: 7.0% Identity: 18% Fold: Adenine nucleotide alpha hydrolase-like Superfamily: Nucleotidylyl transferase Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain Phyre2 PDB 1mhs chain A Region: 11 - 87 Aligned: 69 Modelled: 77 Confidence: 7.0% Identity: 16% PDB header:membrane protein, proton transport Chain: A: PDB Molecule:plasma membrane atpase; PDBTitle: model of neurospora crassa proton atpase Phyre2 PDB 1cii chain A Region: 12 - 80 Aligned: 68 Modelled: 69 Confidence: 6.8% Identity: 9% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 1rut chain X domain 1 Region: 5 - 13 Aligned: 9 Modelled: 9 Confidence: 5.8% Identity: 22% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 3h3h chain A Region: 128 - 195 Aligned: 66 Modelled: 68 Confidence: 5.8% Identity: 14% PDB header:unknown function Chain: A: PDB Molecule:uncharacterized snoal-like protein; PDBTitle: crystal structure of a snoal-like protein of unknown function2 (bth_ii0226) from burkholderia thailandensis e264 at 1.60 a3 resolution Phyre2 PDB 2rdd chain B Region: 339 - 358 Aligned: 20 Modelled: 20 Confidence: 5.6% Identity: 25% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 1g3n chain C domain 1 Region: 5 - 35 Aligned: 31 Modelled: 31 Confidence: 5.4% Identity: 16% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 2cch chain B domain 1 Region: 5 - 35 Aligned: 31 Modelled: 31 Confidence: 5.3% Identity: 16% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 1b0n chain A domain 1 Region: 93 - 102 Aligned: 10 Modelled: 10 Confidence: 5.3% Identity: 30% Fold: Dimerisation interlock Superfamily: SinR repressor dimerisation domain-like Family: SinR repressor dimerisation domain-like Phyre2 PDB 3jvo chain A Region: 69 - 88 Aligned: 20 Modelled: 20 Confidence: 5.2% Identity: 20% PDB header:viral protein Chain: A: PDB Molecule:gp6; PDBTitle: crystal structure of bacteriophage hk97 gp6 Phyre2 1 c3my2A_ 2 c2rdcA_ 3 d1utca2 4 d1oeda_ 5 c2voyH_ 6 c1c9lA_ 7 c1bpoA_ 8 d1f5qb1 9 d1j1ua_ 10 c1mhsA_ 11 c1ciiA_ 12 d1rutx1 13 c3h3hA_ 14 c2rddB_ 15 d1g3nc1 16 d2cchb1 17 d1b0na1 18 c3jvoA_

Detailed template information

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

1 c3my2A_ 50.9 12 PDB header:transport protein Chain: A: PDB Molecule:lipopolysaccharide export system protein lptc; PDBTitle: crystal structure of lptc 2 c2rdcA_ 14.4 42 PDB header:lipid binding protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative lipid binding protein (gsu0061) from2 geobacter sulfurreducens pca at 1.80 a resolution 3 d1utca2 12.6 17 Fold:7-bladed beta-propeller Superfamily:Clathrin heavy-chain terminal domain Family:Clathrin heavy-chain terminal domain 4 d1oeda_ 10.3 7 Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore 5 c2voyH_ 8.8 14 PDB header:hydrolase Chain: H: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 6 c1c9lA_ 8.6 15 PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:clathrin; PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin 7 c1bpoA_ 8.5 17 PDB header:membrane protein Chain: A: PDB Molecule:protein (clathrin); PDBTitle: clathrin heavy-chain terminal domain and linker 8 d1f5qb1 8.0 19 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 9 d1j1ua_ 7.0 18 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain 10 c1mhsA_ 7.0 16 PDB header:membrane protein, proton transport Chain: A: PDB Molecule:plasma membrane atpase; PDBTitle: model of neurospora crassa proton atpase 11 c1ciiA_ 6.8 9 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 12 d1rutx1 5.8 22 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 13 c3h3hA_ 5.8 14 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized snoal-like protein; PDBTitle: crystal structure of a snoal-like protein of unknown function2 (bth_ii0226) from burkholderia thailandensis e264 at 1.60 a3 resolution 14 c2rddB_ 5.6 25 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 15 d1g3nc1 5.4 16 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 16 d2cchb1 5.3 16 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 17 d1b0na1 5.3 30 Fold:Dimerisation interlock Superfamily:SinR repressor dimerisation domain-like Family:SinR repressor dimerisation domain-like 18 c3jvoA_ 5.2 20 PDB header:viral protein Chain: A: PDB Molecule:gp6; PDBTitle: crystal structure of bacteriophage hk97 gp6

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