Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	T	R	T	P	S	S	S	S	S	R	L	M	L	T	I	G	L	C	F	L	V	A	L	M	E	G	L	D	L	Q	A	A	G	I	A	A	G	G	I	A	Q	A	F	A	L	D	K	M	Q	M	G	W	I	F	S	A	G	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	G	L	L	P	G	A	L	V	G	G	M	L	A	D	R	Y	G	R	K	R	I	L	I	G	S	V	A	L	F	G	L	F	S	L	A	T	A	I	A	W	D	F	P	S	L	V	F	A	R	L	M	T	G	V	G	L	G	A	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	P	N	L	I	A	L	T	S	E	A	A	G	P	R	F	R	G	T	A	V	S	L	M	Y	C	G	V	P	I	G	A	A	L	A	A	T	L	G	F	A	G	A	N	L	A	W	Q	T	V	F	W	V	G	G	V	V	P	L	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	V	P	L	L	M	R	W	L	P	E	S	A	V	F	A	G	E	K	Q	S	A	P	P	L	R	A	L	F	A	P	E	T	A	T	A	T	L	L	L	W	L	C	Y	F	F	T	L	L	V	V	Y	M	L	I	N	W	L	P	L
Secondary structure
SS confidence
Disorder																	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	L	V	E	Q	G	F	Q	P	S	Q	A	A	G	V	M	F	A	L	Q	M	G	A	A	S	G	T	L	M	L	G	A	L	M	D	K	L	R	P	V	T	M	S	L	L	I	Y	S	G	M	L	A	S	L	L	A	L	G	T	V
Secondary structure
SS confidence
Disorder						?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		S	S	F	N	G	M	L	L	A	G	F	V	A	G	L	F	A	T	G	G	Q	S	V	L	Y	A	L	A	P	L	F	Y	S	S	Q	I	R	A	T	G	V	G	T	A	V	A	V	G	R	L	G	A	M	S	G	P	L	L	A	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.
Sequence		K	M	L	A	L	G	T	G	T	V	G	V	M	A	A	S	A	P	G	I	L	V	A	G	L	A	V	F	I	L	M	S	R	R	S	R	I	Q	P	C	A	D	A
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: 2 - 402 Aligned: 400 Modelled: 401 Confidence: 100.0% Identity: 14% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2gfp chain A Region: 16 - 382 Aligned: 366 Modelled: 367 Confidence: 100.0% Identity: 14% 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: 10 - 403 Aligned: 391 Modelled: 394 Confidence: 100.0% Identity: 16% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 3o7p chain A Region: 11 - 393 Aligned: 377 Modelled: 383 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: 17 - 389 Aligned: 373 Modelled: 373 Confidence: 100.0% Identity: 11% 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: 15.6% 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 3pro chain C domain 1 Region: 37 - 78 Aligned: 42 Modelled: 42 Confidence: 5.7% Identity: 7% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 PDB 2bbj chain B Region: 328 - 394 Aligned: 67 Modelled: 67 Confidence: 5.6% Identity: 12% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 1qa4 chain A Region: 390 - 402 Aligned: 13 Modelled: 13 Confidence: 5.2% Identity: 38% PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 nef anchor domain (2-57)); PDBTitle: hiv-1 nef anchor domain, nmr, 2 structures Phyre2 1 d1pw4a_ 2 c2gfpA_ 3 d1pv7a_ 4 c3o7pA_ 5 c2xutC_ 6 c2g9pA_ 7 d3proc1 8 c2bbjB_ 9 c1qa4A_

Detailed template information

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

1 d1pw4a_ 100.0 14 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 c2gfpA_ 100.0 14 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 16 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_ 100.0 11 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_ 15.6 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 d3proc1 5.7 7 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 8 c2bbjB_ 5.6 12 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 9 c1qa4A_ 5.2 38 PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 nef anchor domain (2-57)); PDBTitle: hiv-1 nef anchor domain, nmr, 2 structures

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