Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	K	E	N	I	T	I	D	P	R	S	S	F	T	P	S	S	S	A	D	I	P	V	P	P	D	G	L	V	Q	R	S	T	R	I	K	R	I	Q	T	T	A	M	L	L	L	F	F	A	A	V	I	N	Y	L	D	R	S	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	S	V	A	N	L	T	I	R	E	E	L	G	L	S	A	T	E	I	G	A	L	L	S	V	F	S	L	A	Y	G	I	A	Q	L	P	C	G	P	L	L	D	R	K	G	P	R	L	M	L	G	L	G	M	F	F	W	S	L	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Q	A	M	S	G	M	V	H	N	F	T	Q	F	V	L	V	R	I	G	M	G	I	G	E	A	P	M	N	P	C	G	V	K	V	I	N	D	W	F	N	I	K	E	R	G	R	P	M	G	F	F	N	A	A	S	T	I	G	V	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	S	P	P	I	L	A	A	M	M	L	V	M	G	W	R	G	M	F	I	T	I	G	V	L	G	I	F	L	A	I	G	W	Y	M	L	Y	R	N	R	E	H	V	E	L	T	A	V	E	Q	A	Y	L	N	A	G	S	V	N	A
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?									?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		R	R	D	P	L	S	F	A	E	W	R	S	L	F	R	N	R	T	M	W	G	M	M	L	G	F	S	G	I	N	Y	T	A	W	L	Y	L	A	W	L	P	G	Y	L	Q	T	A	Y	N	L	D	L	K	S	T	G	L	M	A	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		I	P	F	L	F	G	A	A	G	M	L	V	N	G	Y	V	T	D	W	L	V	K	G	G	M	A	P	I	K	S	R	K	I	C	I	I	A	G	M	F	C	S	A	A	F	T	L	I	V	P	Q	A	T	T	S	M	T	A	V	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		L	I	G	M	A	L	F	C	I	H	F	A	G	T	S	C	W	G	L	I	H	V	A	V	A	S	R	M	T	A	S	V	G	S	I	Q	N	F	A	S	F	I	C	A	S	F	A	P	I	I	T	G	F	I	V	D	T	T	H	S
Secondary structure
SS confidence
Disorder																									?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.
Sequence		F	R	L	A	L	I	I	C	G	C	V	T	A	A	G	A	L	A	Y	I	F	L	V	R	Q	P	I	N	D	P	R	K	D
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: 21 - 453 Aligned: 419 Modelled: 433 Confidence: 100.0% Identity: 16% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1pv7 chain A Region: 36 - 453 Aligned: 408 Modelled: 418 Confidence: 100.0% Identity: 11% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 2gfp chain A Region: 43 - 434 Aligned: 369 Modelled: 376 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 3o7p chain A Region: 46 - 444 Aligned: 387 Modelled: 399 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: 45 - 439 Aligned: 395 Modelled: 395 Confidence: 100.0% 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 2g9p chain A Region: 96 - 109 Aligned: 14 Modelled: 14 Confidence: 12.7% 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 3pro chain C domain 1 Region: 64 - 105 Aligned: 42 Modelled: 42 Confidence: 11.4% Identity: 17% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 PDB 2rdd chain B Region: 428 - 453 Aligned: 26 Modelled: 26 Confidence: 7.2% Identity: 15% 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 2axt chain I domain 1 Region: 424 - 453 Aligned: 30 Modelled: 30 Confidence: 6.7% Identity: 13% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein I, PsbI Family: PsbI-like Phyre2 PDB 3b9y chain A Region: 326 - 453 Aligned: 125 Modelled: 128 Confidence: 6.1% 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 3prq chain T Region: 426 - 452 Aligned: 27 Modelled: 27 Confidence: 5.8% Identity: 11% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer Phyre2 PDB 3bz2 chain T Region: 426 - 452 Aligned: 27 Modelled: 27 Confidence: 5.8% Identity: 11% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer Phyre2 PDB 3bz1 chain T Region: 426 - 452 Aligned: 27 Modelled: 27 Confidence: 5.8% Identity: 11% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 1 d1pw4a_ 2 d1pv7a_ 3 c2gfpA_ 4 c3o7pA_ 5 c2xutC_ 6 c2g9pA_ 7 d3proc1 8 c2rddB_ 9 d2axti1 10 c3b9yA_ 11 c3prqT_ 12 c3bz2T_ 13 c3bz1T_

Detailed template information

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

1 d1pw4a_ 100.0 16 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 d1pv7a_ 100.0 11 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 3 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 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 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 c2g9pA_ 12.7 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 7 d3proc1 11.4 17 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 8 c2rddB_ 7.2 15 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 d2axti1 6.7 13 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein I, PsbI Family:PsbI-like 10 c3b9yA_ 6.1 8 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 11 c3prqT_ 5.8 11 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 12 c3bz2T_ 5.8 11 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 13 c3bz1T_ 5.8 11 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer

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