Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	N	P	Y	F	P	T	A	L	G	L	Y	F	N	Y	L	V	H	G	M	G	V	L	L	M	S	L	N	M	A	S	L	E	T	L	W	Q	T	N	A	A	G	V	S	I	V	I	S	S	L	G	I	G	R	L	S	V	L	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	A	G	L	L	S	D	R	F	G	R	R	P	F	I	M	L	G	M	C	C	Y	M	A	F	F	F	G	I	L	Q	T	N	N	I	I	I	A	Y	V	F	G	F	L	A	G	M	A	N	S	F	L	D	A	G	T	Y	P	S	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	E	A	F	P	R	S	P	G	T	A	N	I	L	I	K	A	F	V	S	S	G	Q	F	L	L	P	L	I	I	S	L	L	V	W	A	E	L	W	F	G	W	S	F	M	I	A	A	G	I	M	F	I	N	A	L	F	L	Y	R
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		C	T	F	P	P	H	P	G	R	R	L	P	V	I	K	K	T	T	S	S	T	E	H	R	C	S	I	I	D	L	A	S	Y	T	L	Y	G	Y	I	S	M	A	T	F	Y	L	V	S	Q	W	L	A	Q	Y	G	Q	F	V	A	G
Secondary structure
SS confidence
Disorder				?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?					?																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		M	S	Y	T	M	S	I	K	L	L	S	I	Y	T	V	G	S	L	L	C	V	F	I	T	A	P	L	I	R	N	T	V	R	P	T	T	L	L	M	L	Y	T	F	I	S	F	I	A	L	F	T	V	C	L	H	P	T	F	Y	V
Secondary structure
SS confidence
Disorder		?																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	I	I	F	A	F	V	I	G	F	T	S	A	G	G	V	V	Q	I	G	L	T	L	M	A	E	R	F	P	Y	A	K	G	K	A	T	G	I	Y	Y	S	A	G	S	I	A	T	F	T	I	P	L	I	T	A	H	L	S	Q	R
Secondary structure
SS confidence
Disorder																											?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.
Sequence		S	I	A	D	I	M	W	F	D	T	A	I	A	A	I	G	F	L	L	A	L	F	I	G	L	R	S	R	K	K	T	R	H	H	S	L	K	E	N	V	A	P	G	G
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 1pw4 chain A Region: 2 - 400 Aligned: 398 Modelled: 399 Confidence: 100.0% Identity: 16% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1pv7 chain A Region: 1 - 401 Aligned: 401 Modelled: 401 Confidence: 100.0% Identity: 11% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 2gfp chain A Region: 9 - 378 Aligned: 369 Modelled: 370 Confidence: 100.0% Identity: 14% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 3o7p chain A Region: 3 - 388 Aligned: 380 Modelled: 386 Confidence: 100.0% Identity: 9% PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) Phyre2 PDB 2xut chain C Region: 10 - 384 Aligned: 375 Modelled: 375 Confidence: 100.0% Identity: 12% PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. Phyre2 PDB 3qnq chain D Region: 351 - 402 Aligned: 52 Modelled: 52 Confidence: 58.9% Identity: 15% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 3b9y chain A Region: 201 - 398 Aligned: 198 Modelled: 198 Confidence: 47.2% Identity: 14% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 3rko chain N Region: 2 - 402 Aligned: 387 Modelled: 387 Confidence: 39.9% Identity: 9% PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2g9p chain A Region: 61 - 74 Aligned: 14 Modelled: 14 Confidence: 14.5% Identity: 36% PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom Phyre2 PDB 2knc chain A Region: 364 - 399 Aligned: 36 Modelled: 36 Confidence: 7.3% Identity: 8% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2rdd chain B Region: 369 - 399 Aligned: 31 Modelled: 31 Confidence: 7.2% Identity: 16% 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 1 d1pw4a_ 2 d1pv7a_ 3 c2gfpA_ 4 c3o7pA_ 5 c2xutC_ 6 c3qnqD_ 7 c3b9yA_ 8 c3rkoN_ 9 c2g9pA_ 10 c2kncA_ 11 c2rddB_

Detailed template information

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

1 d1pw4a_ 100.0 16 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 d1pv7a_ 100.0 11 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 3 c2gfpA_ 100.0 14 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 4 c3o7pA_ 100.0 9 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 5 c2xutC_ 100.0 12 PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. 6 c3qnqD_ 58.9 15 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 7 c3b9yA_ 47.2 14 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 8 c3rkoN_ 39.9 9 PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 9 c2g9pA_ 14.5 36 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom 10 c2kncA_ 7.3 8 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 11 c2rddB_ 7.2 16 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.

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