Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	T	T	Q	T	S	T	I	A	S	K	D	S	R	S	A	W	R	K	T	D	T	M	W	M	L	G	L	Y	G	T	A	I	G	A	G	V	L	F	L	P	I	N	A	G	V	G	G	M	I	P	L	I	I	M	A	I	L	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	P	M	T	F	F	A	H	R	G	L	T	R	F	V	L	S	G	K	N	P	G	E	D	I	T	E	V	V	E	E	H	F	G	I	G	A	G	K	L	I	T	L	L	Y	F	F	A	I	Y	P	I	L	L	V	Y	S	V	A	I
Secondary structure
SS confidence
Disorder																		?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	N	T	V	E	S	F	M	S	H	Q	L	G	M	T	P	P	P	R	A	I	L	S	L	I	L	I	V	G	M	M	T	I	V	R	F	G	E	Q	M	I	V	K	A	M	S	I	L	V	F	P	F	V	G	V	L	M	L	L	A
Secondary structure
SS confidence
Disorder															?																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	Y	L	I	P	Q	W	N	G	A	A	L	E	T	L	S	L	D	T	A	S	A	T	G	N	G	L	W	M	T	L	W	L	A	I	P	V	M	V	F	S	F	N	H	S	P	I	I	S	S	F	A	V	A	K	R	E	E	Y	G
Secondary structure
SS confidence
Disorder						?		?		?	?	?	?		?		?	?	?	?	?	?	?	?	?	?	?		?																													?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		D	M	A	E	Q	K	C	S	K	I	L	A	F	A	H	I	M	M	V	L	T	V	M	F	F	V	F	S	C	V	L	S	L	T	P	A	D	L	A	A	A	K	E	Q	N	I	S	I	L	S	Y	L	A	N	H	F	N	A	P	V
Secondary structure
SS confidence
Disorder		?	?																																	?						?	?	?	?											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		I	A	W	M	A	P	I	I	A	I	I	A	I	T	K	S	F	L	G	H	Y	L	G	A	R	E	G	F	N	G	M	V	I	K	S	L	R	G	K	G	K	S	I	E	I	N	K	L	N	R	I	T	A	L	F	M	L	V	T	T
Secondary structure
SS confidence
Disorder																																						?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		W	I	V	A	T	L	N	P	S	I	L	G	M	I	E	T	L	G	G	P	I	I	A	M	I	L	F	L	M	P	M	Y	A	I	Q	K	V	P	A	M	R	K	Y	S	G	H	I	S	N	V	F	V	V	V	M	G	L	I	A	I
Secondary structure
SS confidence
Disorder																																									?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		S	A	I	F	Y	S	L	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: 16 - 427 Aligned: 393 Modelled: 411 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: 17 - 425 Aligned: 372 Modelled: 372 Confidence: 100.0% Identity: 13% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 5 - 424 Aligned: 399 Modelled: 399 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 3dh4 chain A Region: 2 - 425 Aligned: 411 Modelled: 397 Confidence: 99.3% 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 2xq2 chain A Region: 18 - 425 Aligned: 396 Modelled: 396 Confidence: 99.1% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 PDB 2a65 chain A domain 1 Region: 20 - 426 Aligned: 395 Modelled: 395 Confidence: 98.6% Identity: 14% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2w8a chain C Region: 8 - 406 Aligned: 389 Modelled: 399 Confidence: 98.3% 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 - 401 Aligned: 396 Modelled: 398 Confidence: 97.2% Identity: 8% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 3hd7 chain A Region: 396 - 429 Aligned: 34 Modelled: 34 Confidence: 10.4% Identity: 12% PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 Phyre2 PDB 2zkr chain 3 Region: 6 - 24 Aligned: 19 Modelled: 19 Confidence: 7.7% Identity: 26% PDB header:ribosomal protein/rna Chain: 3: PDB Molecule:60s ribosomal protein l39e; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 1vqo chain 2 domain 1 Region: 8 - 22 Aligned: 15 Modelled: 15 Confidence: 7.3% Identity: 33% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Ribosomal protein L39e Family: Ribosomal protein L39e Phyre2 PDB 4a1b chain B Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 6.9% Identity: 21% PDB header:ribosome Chain: B: PDB Molecule:rpl39; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 3. Phyre2 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 c3dh4A_ 5 c2xq2A_ 6 d2a65a1 7 c2w8aC_ 8 c3hfxA_ 9 c3hd7A_ 10 c2zkr3_ 11 d1vqo21 12 c4a1bB_

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 13 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 c3dh4A_ 99.3 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 5 c2xq2A_ 99.1 11 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 6 d2a65a1 98.6 14 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 7 c2w8aC_ 98.3 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_ 97.2 8 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 c3hd7A_ 10.4 12 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 10 c2zkr3_ 7.7 26 PDB header:ribosomal protein/rna Chain: 3: PDB Molecule:60s ribosomal protein l39e; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 11 d1vqo21 7.3 33 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Ribosomal protein L39e Family:Ribosomal protein L39e 12 c4a1bB_ 6.9 21 PDB header:ribosome Chain: B: PDB Molecule:rpl39; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 3.

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