Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	I	P	V	N	A	A	K	P	G	R	R	R	Y	L	T	L	V	M	I	F	I	T	V	V	I	C	Y	V	D	R	A	N	L	A	V	A	S	A	H	I	Q	E	E	F	G	I	T	K	A	E	M	G	Y	V	F	S	A	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	W	L	Y	T	L	C	Q	I	P	G	G	W	F	L	D	R	V	G	S	R	V	T	Y	F	I	A	I	F	G	W	S	V	A	T	L	F	Q	G	F	A	T	G	L	M	S	L	I	G	L	R	A	I	T	G	I	F	E	A	P
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	F	P	T	N	N	R	M	V	T	S	W	F	P	E	H	E	R	A	S	A	V	G	F	Y	T	S	G	Q	F	V	G	L	A	F	L	T	P	L	L	I	W	I	Q	E	M	L	S	W	H	W	V	F	I	V	T	G	G	I	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	I	W	S	L	I	W	F	K	V	Y	Q	P	P	R	L	T	K	G	I	S	K	A	E	L	D	Y	I	R	D	G	G	G	L	V	D	G	D	A	P	V	K	K	E	A	R	Q	P	L	T	A	K	D	W	K	L	V	F	H	R
Secondary structure
SS confidence
Disorder																			?	?											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		K	L	I	G	V	Y	L	G	Q	F	A	V	A	S	T	L	W	F	F	L	T	W	F	P	N	Y	L	T	Q	E	K	G	I	T	A	L	K	A	G	F	M	T	T	V	P	F	L	A	A	F	V	G	V	L	L	S	G	W	V	A
Secondary structure
SS confidence
Disorder																																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		D	L	L	V	R	K	G	F	S	L	G	F	A	R	K	T	P	I	I	C	G	L	L	I	S	T	C	I	M	G	A	N	Y	T	N	D	P	M	M	I	M	C	L	M	A	L	A	F	F	G	N	G	F	A	S	I	T	W	S	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		V	S	S	L	A	P	M	R	L	I	G	L	T	G	G	V	F	N	F	A	G	G	L	G	G	I	T	V	P	L	V	V	G	Y	L	A	Q	G	Y	G	F	A	P	A	L	V	Y	I	S	A	V	A	L	I	G	A	L	S	Y	I
Secondary structure
SS confidence
Disorder						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430
Sequence		L	L	V	G	D	V	K	R	V	G
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: 1 - 428 Aligned: 409 Modelled: 412 Confidence: 100.0% Identity: 18% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 3o7p chain A Region: 12 - 426 Aligned: 401 Modelled: 411 Confidence: 100.0% Identity: 15% 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: 17 - 415 Aligned: 369 Modelled: 374 Confidence: 100.0% Identity: 15% 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: 14 - 429 Aligned: 400 Modelled: 416 Confidence: 100.0% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 2xut chain C Region: 19 - 422 Aligned: 404 Modelled: 404 Confidence: 100.0% 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 3b9y chain A Region: 9 - 237 Aligned: 221 Modelled: 229 Confidence: 80.6% 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 2g9p chain A Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 16.0% Identity: 14% 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 1u7g chain A Region: 4 - 160 Aligned: 150 Modelled: 157 Confidence: 10.1% Identity: 14% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 3a0b chain T Region: 406 - 429 Aligned: 24 Modelled: 24 Confidence: 6.2% Identity: 8% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1s5l chain T Region: 406 - 429 Aligned: 24 Modelled: 24 Confidence: 6.2% Identity: 8% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 1s5l chain T Region: 406 - 429 Aligned: 24 Modelled: 24 Confidence: 6.2% Identity: 8% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3arc chain T Region: 402 - 429 Aligned: 28 Modelled: 28 Confidence: 5.9% Identity: 7% PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3a0b chain T Region: 402 - 429 Aligned: 28 Modelled: 28 Confidence: 5.9% Identity: 7% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 1 d1pw4a_ 2 c3o7pA_ 3 c2gfpA_ 4 d1pv7a_ 5 c2xutC_ 6 c3b9yA_ 7 c2g9pA_ 8 d1u7ga_ 9 c3a0bt_ 10 c1s5lt_ 11 c1s5lT_ 12 c3arct_ 13 c3a0bT_

Detailed template information

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

1 d1pw4a_ 100.0 18 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 c3o7pA_ 100.0 15 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 3 c2gfpA_ 100.0 15 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 4 d1pv7a_ 100.0 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 5 c2xutC_ 100.0 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 c3b9yA_ 80.6 8 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 7 c2g9pA_ 16.0 14 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 8 d1u7ga_ 10.1 14 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 9 c3a0bt_ 6.2 8 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 10 c1s5lt_ 6.2 8 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 11 c1s5lT_ 6.2 8 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 12 c3arct_ 5.9 7 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 13 c3a0bT_ 5.9 7 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex

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