Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	D	Q	A	E	K	K	H	S	A	F	W	G	V	M	V	I	A	G	T	V	I	G	G	G	M	F	A	L	P	V	D	L	A	G	A	W	F	F	W	G	A	F	I	L	I	I	A	W	F	S	M	L	H	S	G	L	L	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																										?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	E	A	N	L	N	Y	P	V	G	S	S	F	N	T	I	T	K	D	L	I	G	N	T	W	N	I	I	S	G	I	T	V	A	F	V	L	Y	I	L	T	Y	A	Y	I	S	A	N	G	A	I	I	S	E	T	I	S	M	N	L
Secondary structure
SS confidence
Disorder						?	?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	Y	H	A	N	P	R	I	V	G	I	C	T	A	I	F	V	A	S	V	L	W	L	S	S	L	A	A	S	R	I	T	S	L	F	L	G	L	K	I	I	S	F	V	I	V	F	G	S	F	F	F	Q	V	D	Y	S	I	L	R
Secondary structure
SS confidence
Disorder																								?	?	?																															?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		D	A	T	S	S	T	A	G	T	S	Y	F	P	Y	I	F	M	A	L	P	V	C	L	A	S	F	G	F	H	G	N	I	P	S	L	I	I	C	Y	G	K	R	K	D	K	L	I	K	S	V	V	F	G	S	L	L	A	L	V	I
Secondary structure
SS confidence
Disorder		?		?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		Y	L	F	W	L	Y	C	T	M	G	N	I	P	R	E	S	F	K	A	I	I	S	S	G	G	N	V	D	S	L	V	K	S	F	L	G	T	K	Q	H	G	I	I	E	F	C	L	L	V	F	S	N	L	A	V	A	S	S	F	F
Secondary structure
SS confidence
Disorder																					?	?	?	?			?	?										?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	V	T	L	G	L	F	D	Y	L	A	D	L	F	K	I	D	N	S	H	G	G	R	F	K	T	V	L	L	T	F	L	P	P	A	L	L	Y	L	I	F	P	N	G	F	I	Y	G	I	G	G	A	G	L	C	A	T	I	W	A
Secondary structure
SS confidence
Disorder																	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.
Sequence		V	I	I	P	A	V	L	A	I	K	A	R	K	K	F	P	N	Q	M	F	T	V	W	G	G	N	L	I	P	A	I	V	I	L	F	G	I	T	V	I	L	C	W	F	G	N	V	F	N	V	L	P	K	F	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: 5 - 411 Aligned: 399 Modelled: 407 Confidence: 100.0% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3lrc chain C Region: 5 - 401 Aligned: 374 Modelled: 374 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: 2 - 413 Aligned: 406 Modelled: 410 Confidence: 99.9% Identity: 8% 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: 7 - 405 Aligned: 383 Modelled: 383 Confidence: 98.8% Identity: 11% 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: 3 - 405 Aligned: 388 Modelled: 401 Confidence: 98.7% Identity: 11% 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: 10 - 413 Aligned: 401 Modelled: 404 Confidence: 98.0% Identity: 15% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2w8a chain C Region: 2 - 381 Aligned: 375 Modelled: 380 Confidence: 96.9% Identity: 11% 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 - 378 Aligned: 370 Modelled: 370 Confidence: 62.0% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 1llc chain A domain 1 Region: 1 - 35 Aligned: 24 Modelled: 35 Confidence: 10.7% Identity: 25% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: LDH N-terminal domain-like Phyre2 PDB 1s0y chain A Region: 2 - 24 Aligned: 21 Modelled: 23 Confidence: 9.7% Identity: 29% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: 4-oxalocrotonate tautomerase-like Phyre2 PDB 1byy chain A Region: 1 - 7 Aligned: 7 Modelled: 7 Confidence: 7.7% Identity: 43% PDB header:membrane protein Chain: A: PDB Molecule:protein (sodium channel alpha-subunit); PDBTitle: sodium channel iia inactivation gate Phyre2 PDB 3qe7 chain A Region: 84 - 367 Aligned: 284 Modelled: 284 Confidence: 7.5% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:uracil permease; PDBTitle: crystal structure of uracil transporter--uraa Phyre2 PDB 1v92 chain A Region: 1 - 15 Aligned: 15 Modelled: 15 Confidence: 5.7% Identity: 20% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: TAP-C domain-like Phyre2 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 c2xq2A_ 5 c3dh4A_ 6 d2a65a1 7 c2w8aC_ 8 c3hfxA_ 9 d1llca1 10 d1s0ya_ 11 c1byyA_ 12 c3qe7A_ 13 d1v92a_

Detailed template information

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

1 c3giaA_ 100.0 13 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 8 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 c2xq2A_ 98.8 11 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 5 c3dh4A_ 98.7 11 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 98.0 15 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 7 c2w8aC_ 96.9 11 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_ 62.0 10 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 d1llca1 10.7 25 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like 10 d1s0ya_ 9.7 29 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like 11 c1byyA_ 7.7 43 PDB header:membrane protein Chain: A: PDB Molecule:protein (sodium channel alpha-subunit); PDBTitle: sodium channel iia inactivation gate 12 c3qe7A_ 7.5 11 PDB header:transport protein Chain: A: PDB Molecule:uracil permease; PDBTitle: crystal structure of uracil transporter--uraa 13 d1v92a_ 5.7 20 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:TAP-C domain-like

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