Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	N	I	W	S	K	E	E	T	L	W	S	F	A	L	Y	G	T	A	V	G	A	G	T	L	F	L	P	I	Q	L	G	S	A	G	A	V	V	L	F	I	T	A	L	V	A	W	P	L	T	Y	W	P	H	K	A	L	C	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																											?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	I	L	S	S	K	T	S	A	G	E	G	I	T	G	A	V	T	H	Y	Y	G	K	K	I	G	N	L	I	T	T	L	Y	F	I	A	F	F	V	V	V	L	I	Y	A	V	A	I	T	N	S	L	T	E	Q	L	A	K	H	M
Secondary structure
SS confidence
Disorder					?	?			?	?	?																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	I	D	L	R	I	R	M	L	V	S	L	G	V	V	L	I	L	N	L	I	F	L	M	G	R	H	A	T	I	R	V	M	G	F	L	V	F	P	L	I	A	Y	F	L	F	L	S	I	Y	L	V	G	S	W	Q	P	D	L	L
Secondary structure
SS confidence
Disorder			?		?		?																		?																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		T	T	Q	V	E	F	N	Q	N	T	L	H	Q	I	W	I	S	I	P	V	M	V	F	A	F	S	H	T	P	I	I	S	T	F	A	I	D	R	R	E	K	Y	G	E	H	A	M	D	K	C	K	K	I	M	K	V	A	Y	L	I
Secondary structure
SS confidence
Disorder			?			?	?	?	?																																	?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	C	I	S	V	L	F	F	V	F	S	C	L	L	S	I	P	P	S	Y	I	E	A	A	K	E	E	G	V	T	I	L	S	A	L	S	M	L	P	N	A	P	A	W	L	S	I	S	G	I	I	V	A	V	V	A	M	S	K	S
Secondary structure
SS confidence
Disorder																									?		?	?											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		F	L	G	T	Y	F	G	V	I	E	G	A	T	E	V	V	K	T	T	L	Q	Q	V	G	V	K	K	S	R	A	F	N	R	A	L	S	I	M	L	V	S	L	I	T	F	I	V	C	C	I	N	P	N	A	I	S	M	I	Y	A
Secondary structure
SS confidence
Disorder																						?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.
Sequence		I	S	G	P	L	I	A	M	I	L	F	I	M	P	T	L	S	T	Y	L	I	P	A	L	K	P	W	R	S	I	G	N	L	I	T	L	I	V	G	I	L	C	V	S	V	M	F	F	S
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: 6 - 408 Aligned: 387 Modelled: 397 Confidence: 100.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3lrc chain C Region: 6 - 409 Aligned: 369 Modelled: 369 Confidence: 100.0% Identity: 14% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 3 - 409 Aligned: 391 Modelled: 391 Confidence: 99.9% Identity: 9% 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: 5 - 408 Aligned: 392 Modelled: 404 Confidence: 99.1% Identity: 10% 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: 6 - 408 Aligned: 392 Modelled: 403 Confidence: 99.1% 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 - 389 Aligned: 376 Modelled: 386 Confidence: 98.7% Identity: 12% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2w8a chain C Region: 8 - 391 Aligned: 373 Modelled: 356 Confidence: 95.9% 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: 22 - 386 Aligned: 355 Modelled: 355 Confidence: 76.4% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 1o9a chain A domain 1 Region: 1 - 8 Aligned: 8 Modelled: 8 Confidence: 8.0% Identity: 13% Fold: FnI-like domain Superfamily: FnI-like domain Family: Fibronectin type I module Phyre2 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 c2xq2A_ 5 c3dh4A_ 6 d2a65a1 7 c2w8aC_ 8 c3hfxA_ 9 d1o9aa1

Detailed template information

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

1 c3giaA_ 100.0 11 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 2 c3lrcC_ 100.0 14 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 3 c2jlnA_ 99.9 9 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 c2xq2A_ 99.1 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 5 c3dh4A_ 99.1 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 98.7 12 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 7 c2w8aC_ 95.9 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_ 76.4 12 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 d1o9aa1 8.0 13 Fold:FnI-like domain Superfamily:FnI-like domain Family:Fibronectin type I module

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