Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	H	N	S	Y	R	R	W	I	T	L	A	I	I	S	F	S	G	G	V	S	F	D	L	A	Y	L	R	Y	I	Y	Q	I	P	M	A	K	F	M	G	F	S	N	T	E	I	G	L	I	M	S	T	F	G	I	A	A	I	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	Y	A	P	S	G	V	I	A	D	K	F	S	H	R	K	M	I	T	S	A	M	I	I	T	G	L	L	G	L	L	M	A	T	Y	P	P	L	W	V	M	L	C	I	Q	I	A	F	A	I	T	T	I	L	M	L	W	S	V	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	K	A	A	S	L	L	G	D	H	S	E	Q	G	K	I	M	G	W	M	E	G	L	R	G	V	G	V	M	S	L	A	V	F	T	M	W	V	F	S	R	F	A	P	D	D	S	T	S	L	K	T	V	I	I	I	Y	S	V	V
Secondary structure
SS confidence
Disorder																																													?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		Y	I	L	L	G	I	L	C	W	F	F	V	S	D	N	N	N	L	R	S	A	N	N	E	E	K	Q	S	F	Q	L	S	D	I	L	A	V	L	R	I	S	T	T	W	Y	C	S	M	V	I	F	G	V	F	T	I	Y	A	I	L
Secondary structure
SS confidence
Disorder																	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	Y	S	T	N	Y	L	T	E	M	Y	G	M	S	L	V	A	A	S	Y	M	G	I	V	I	N	K	I	F	R	A	L	C	G	P	L	G	G	I	I	T	T	Y	S	K	V	K	S	P	T	R	V	I	Q	I	L	S	V	L	G
Secondary structure
SS confidence
Disorder													?																																?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		L	L	T	L	T	A	L	L	V	T	N	S	N	P	Q	S	V	A	M	G	I	G	L	I	L	L	L	G	F	T	C	Y	A	S	R	G	L	Y	W	A	C	P	G	E	A	R	T	P	S	Y	I	M	G	T	T	V	G	I	C	S
Secondary structure
SS confidence
Disorder																																														?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		V	I	G	F	L	P	D	V	F	V	Y	P	I	I	G	H	W	Q	D	T	L	P	A	A	E	A	Y	R	N	M	W	L	M	G	M	A	A	L	G	M	V	I	V	F	T	F	L	L	F	Q	K	I	R	T	A	D	S	A	P	A
Secondary structure
SS confidence
Disorder																																																			?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.
Sequence		M	A	S	S	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: 2 - 422 Aligned: 410 Modelled: 414 Confidence: 100.0% Identity: 13% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1pv7 chain A Region: 1 - 424 Aligned: 414 Modelled: 421 Confidence: 100.0% Identity: 8% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 3o7p chain A Region: 7 - 410 Aligned: 386 Modelled: 401 Confidence: 100.0% Identity: 13% 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 2gfp chain A Region: 12 - 398 Aligned: 369 Modelled: 372 Confidence: 100.0% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 2xut chain C Region: 13 - 407 Aligned: 394 Modelled: 395 Confidence: 99.9% Identity: 10% 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 3mku chain A Region: 3 - 424 Aligned: 422 Modelled: 422 Confidence: 88.6% Identity: 9% PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter Phyre2 PDB 1rh1 chain A domain 2 Region: 2 - 74 Aligned: 71 Modelled: 73 Confidence: 26.3% Identity: 20% Fold: Toxins' membrane translocation domains Superfamily: Colicin Family: Colicin Phyre2 PDB 2rdd chain B Region: 393 - 424 Aligned: 32 Modelled: 32 Confidence: 21.0% Identity: 13% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 3qnq chain D Region: 391 - 425 Aligned: 35 Modelled: 35 Confidence: 13.0% Identity: 6% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 2g9p chain A Region: 64 - 77 Aligned: 14 Modelled: 14 Confidence: 11.8% Identity: 21% 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 2kvl chain A Region: 5 - 20 Aligned: 16 Modelled: 16 Confidence: 7.3% Identity: 6% PDB header:viral protein Chain: A: PDB Molecule:major outer capsid protein vp7; PDBTitle: nmr structure of the c-terminal domain of vp7 Phyre2 PDB 2bbj chain B Region: 358 - 413 Aligned: 53 Modelled: 56 Confidence: 6.8% Identity: 13% 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 3b9y chain A Region: 2 - 217 Aligned: 208 Modelled: 216 Confidence: 6.3% Identity: 8% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 3pro chain C domain 1 Region: 32 - 73 Aligned: 42 Modelled: 42 Confidence: 6.0% Identity: 17% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 1 d1pw4a_ 2 d1pv7a_ 3 c3o7pA_ 4 c2gfpA_ 5 c2xutC_ 6 c3mkuA_ 7 d1rh1a2 8 c2rddB_ 9 c3qnqD_ 10 c2g9pA_ 11 c2kvlA_ 12 c2bbjB_ 13 c3b9yA_ 14 d3proc1

Detailed template information

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

1 d1pw4a_ 100.0 13 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 d1pv7a_ 100.0 8 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 3 c3o7pA_ 100.0 13 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 4 c2gfpA_ 100.0 11 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 5 c2xutC_ 99.9 10 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 c3mkuA_ 88.6 9 PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter 7 d1rh1a2 26.3 20 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 8 c2rddB_ 21.0 13 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 9 c3qnqD_ 13.0 6 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 10 c2g9pA_ 11.8 21 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 11 c2kvlA_ 7.3 6 PDB header:viral protein Chain: A: PDB Molecule:major outer capsid protein vp7; PDBTitle: nmr structure of the c-terminal domain of vp7 12 c2bbjB_ 6.8 13 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 13 c3b9yA_ 6.3 8 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 14 d3proc1 6.0 17 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain

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