Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	T	A	W	Y	K	Q	V	N	P	P	Q	R	K	A	L	F	S	A	W	L	G	Y	V	F	D	G	F	D	F	M	M	I	F	Y	I	L	H	I	I	K	A	D	L	G	I	T	D	I	Q	A	T	L	I	G	T	V	A	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																																	?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	A	R	P	I	G	G	G	F	F	G	A	M	A	D	K	Y	G	R	K	P	M	M	M	W	A	I	F	I	Y	S	V	G	T	G	L	S	G	I	A	T	N	L	Y	M	L	A	V	C	R	F	I	V	G	L	G	M	S	G	E
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	A	C	A	S	T	Y	A	V	E	S	W	P	K	N	L	Q	S	K	A	S	A	F	L	V	S	G	F	S	V	G	N	I	I	A	A	Q	I	I	P	Q	F	A	E	V	Y	G	W	R	N	S	F	F	I	G	L	L	P	V	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	V	L	W	I	R	K	S	A	P	E	S	Q	E	W	I	E	D	K	Y	K	D	K	S	T	F	L	S	V	F	R	K	P	H	L	S	I	S	M	I	V	F	L	V	C	F	C	L	F	G	A	N	W	P	I	N	G	L	L	P
Secondary structure
SS confidence
Disorder																				?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	Y	L	A	D	N	G	V	N	T	V	V	I	S	T	L	M	T	I	A	G	L	G	T	L	T	G	T	I	F	F	G	F	V	G	D	K	I	G	V	K	K	A	F	V	V	G	L	I	T	S	F	I	F	L	C	P	L	F	F
Secondary structure
SS confidence
Disorder							?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		I	S	V	K	N	S	S	L	I	G	L	C	L	F	G	L	M	F	T	N	L	G	I	A	G	L	V	P	K	F	I	Y	D	Y	F	P	T	K	L	R	G	L	G	T	G	L	I	Y	N	L	G	A	T	G	G	M	A	A	P	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.
Sequence		L	A	T	Y	I	S	G	Y	Y	G	L	G	V	S	L	F	I	V	T	V	A	F	S	A	L	L	I	L	L	V	G	F	D	I	P	G	K	I	Y	K	L	S	V	A	K
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: 7 - 405 Aligned: 398 Modelled: 399 Confidence: 100.0% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2gfp chain A Region: 17 - 386 Aligned: 369 Modelled: 370 Confidence: 100.0% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 1pv7 chain A Region: 9 - 397 Aligned: 387 Modelled: 389 Confidence: 100.0% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 3o7p chain A Region: 15 - 395 Aligned: 379 Modelled: 381 Confidence: 100.0% Identity: 12% 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: 18 - 392 Aligned: 375 Modelled: 375 Confidence: 99.9% 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 2g9p chain A Region: 69 - 82 Aligned: 14 Modelled: 14 Confidence: 16.2% Identity: 43% 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 2bcx chain B Region: 5 - 21 Aligned: 17 Modelled: 17 Confidence: 12.4% Identity: 24% PDB header:calcium binding protein Chain: B: PDB Molecule:ryanodine receptor 1; PDBTitle: crystal structure of calmodulin in complex with a ryanodine2 receptor peptide Phyre2 PDB 1jhf chain A domain 1 Region: 7 - 52 Aligned: 41 Modelled: 41 Confidence: 6.0% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: LexA repressor, N-terminal DNA-binding domain Phyre2 PDB 3cx5 chain C domain 2 Region: 11 - 71 Aligned: 61 Modelled: 61 Confidence: 5.5% Identity: 11% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 1 d1pw4a_ 2 c2gfpA_ 3 d1pv7a_ 4 c3o7pA_ 5 c2xutC_ 6 c2g9pA_ 7 c2bcxB_ 8 d1jhfa1 9 d3cx5c2

Detailed template information

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

1 d1pw4a_ 100.0 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 c2gfpA_ 100.0 13 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 3 d1pv7a_ 100.0 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 4 c3o7pA_ 100.0 12 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_ 99.9 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 c2g9pA_ 16.2 43 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 7 c2bcxB_ 12.4 24 PDB header:calcium binding protein Chain: B: PDB Molecule:ryanodine receptor 1; PDBTitle: crystal structure of calmodulin in complex with a ryanodine2 receptor peptide 8 d1jhfa1 6.0 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain 9 d3cx5c2 5.5 11 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

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