Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	N	R	T	L	G	S	V	F	I	V	A	G	T	T	I	G	A	G	M	L	A	M	P	L	A	A	A	G	V	G	F	S	V	T	L	I	L	L	I	G	L	W	A	L	M	C	Y	T	A	L	L	L	L	E	V	Y	Q	H
Secondary structure
SS confidence
Disorder		?	?	?	?																										?	?	?																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	P	A	D	T	G	L	G	T	L	A	K	R	Y	L	G	R	Y	G	Q	W	L	T	G	F	S	M	M	F	L	M	Y	A	L	T	A	A	Y	I	S	G	A	G	E	L	L	A	S	S	I	S	D	W	T	G	I	S	M	S	A
Secondary structure
SS confidence
Disorder					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	A	G	V	L	L	F	T	F	V	A	G	G	V	V	C	V	G	T	S	L	V	D	L	F	N	R	F	L	F	S	A	K	I	I	F	L	V	V	M	L	V	L	L	L	P	H	I	H	K	V	N	L	L	T	L	P	L	Q	Q
Secondary structure
SS confidence
Disorder																		?		?	?																																			?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	L	A	L	S	A	I	P	V	I	F	T	S	F	G	F	H	G	S	V	P	S	I	V	S	Y	M	D	G	N	I	R	K	L	R	W	V	F	I	I	G	S	A	I	P	L	V	A	Y	I	F	W	Q	V	A	T	L	G	S	I
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		D	S	T	T	F	M	G	L	L	A	N	H	A	G	L	N	G	L	L	Q	A	L	R	E	M	V	A	S	P	H	V	E	L	A	V	H	L	F	A	D	L	A	L	A	T	S	F	L	G	V	A	L	G	L	F	D	Y	L	A	D
Secondary structure
SS confidence
Disorder				?		?	?	?	?	?	?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		L	F	Q	R	S	N	T	V	G	G	R	L	Q	T	G	A	I	T	F	L	P	P	L	A	F	A	L	F	Y	P	R	G	F	V	M	A	L	G	Y	A	G	V	A	L	A	V	L	A	L	I	I	P	S	L	L	T	W	Q	S	R
Secondary structure
SS confidence
Disorder				?	?		?	?	?	?																																																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.
Sequence		K	H	N	P	Q	A	G	Y	R	V	K	G	G	R	P	A	L	V	V	V	F	L	C	G	I	A	V	I	G	V	Q	F	L	I	A	A	G	L	L	P	E	V	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 3gia chain A Region: 1 - 391 Aligned: 387 Modelled: 387 Confidence: 100.0% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3lrc chain C Region: 2 - 389 Aligned: 366 Modelled: 366 Confidence: 100.0% Identity: 15% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 2 - 396 Aligned: 387 Modelled: 387 Confidence: 100.0% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 2xq2 chain A Region: 10 - 393 Aligned: 368 Modelled: 368 Confidence: 99.0% Identity: 9% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 PDB 3dh4 chain A Region: 2 - 393 Aligned: 375 Modelled: 392 Confidence: 98.9% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus Phyre2 PDB 2a65 chain A domain 1 Region: 3 - 400 Aligned: 395 Modelled: 398 Confidence: 98.4% Identity: 14% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2w8a chain C Region: 4 - 369 Aligned: 366 Modelled: 366 Confidence: 96.4% Identity: 12% PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate Phyre2 PDB 3hfx chain A Region: 4 - 365 Aligned: 362 Modelled: 362 Confidence: 84.8% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 1iwg chain A domain 8 Region: 205 - 365 Aligned: 161 Modelled: 161 Confidence: 6.3% Identity: 7% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 c2xq2A_ 5 c3dh4A_ 6 d2a65a1 7 c2w8aC_ 8 c3hfxA_ 9 d1iwga8

Detailed template information

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

1 c3giaA_ 100.0 12 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 2 c3lrcC_ 100.0 15 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 3 c2jlnA_ 100.0 11 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 c2xq2A_ 99.0 9 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 5 c3dh4A_ 98.9 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 6 d2a65a1 98.4 14 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 7 c2w8aC_ 96.4 12 PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate 8 c3hfxA_ 84.8 12 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 d1iwga8 6.3 7 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane 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