Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	T	T	T	Q	N	I	P	W	Y	R	H	L	N	R	A	Q	W	R	A	F	S	A	A	W	L	G	Y	L	L	D	G	F	D	F	V	L	I	A	L	V	L	T	E	V	Q	G	E	F	G	L	T	T	V	Q	A	A	S	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?																																				?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	S	A	A	F	I	S	R	W	F	G	G	L	M	L	G	A	M	G	D	R	Y	G	R	R	L	A	M	V	T	S	I	V	L	F	S	A	G	T	L	A	C	G	F	A	P	G	Y	I	T	M	F	I	A	R	L	V	I	G	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	M	A	G	E	Y	G	S	S	A	T	Y	V	I	E	S	W	P	K	H	L	R	N	K	A	S	G	F	L	I	S	G	F	S	V	G	A	V	V	A	A	Q	V	Y	S	L	V	V	P	V	W	G	W	R	A	L	F	F	I	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	L	P	I	I	F	A	L	W	L	R	K	N	I	P	E	A	E	D	W	K	E	K	H	A	G	K	A	P	V	R	T	M	V	D	I	L	Y	R	G	E	H	R	I	A	N	I	V	M	T	L	A	A	A	T	A	L	W	F	C
Secondary structure
SS confidence
Disorder																								?	?	?	?	?	?											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	A	G	N	L	Q	N	A	A	I	V	A	V	L	G	L	L	C	A	A	I	F	I	S	F	M	V	Q	S	A	G	K	R	W	P	T	G	V	M	L	M	V	V	V	L	F	A	F	L	Y	S	W	P	I	Q	A	L	L	P	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?			?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		Y	L	K	T	D	L	A	Y	N	P	H	T	V	A	N	V	L	F	F	S	G	F	G	A	A	V	G	C	C	V	G	G	F	L	G	D	W	L	G	T	R	K	A	Y	V	C	S	L	L	A	S	Q	L	L	I	I	P	V	F	A
Secondary structure
SS confidence
Disorder						?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		I	G	G	A	N	V	W	V	L	G	L	L	L	F	F	Q	Q	M	L	G	Q	G	I	A	G	I	L	P	K	L	I	G	G	Y	F	D	T	D	Q	R	A	A	G	L	G	F	T	Y	N	V	G	A	L	G	G	A	L	A	P	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		I	G	A	L	I	A	Q	R	L	D	L	G	T	A	L	A	S	L	S	F	S	L	T	F	V	V	I	L	L	I	G	L	D	M	P	S	R	V	Q	R	W	L	R	P	E	A	L	R	T	H	D	A	I	D	G	K	P	F	S	G
Secondary structure
SS confidence
Disorder																																				?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.
Sequence		A	V	P	F	G	S	A	K	N	D	L	V	K	T	K	S
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: 3 - 466 Aligned: 415 Modelled: 416 Confidence: 100.0% Identity: 15% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 3o7p chain A Region: 24 - 457 Aligned: 403 Modelled: 409 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 2gfp chain A Region: 21 - 446 Aligned: 369 Modelled: 370 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 2xut chain C Region: 23 - 454 Aligned: 432 Modelled: 432 Confidence: 100.0% Identity: 9% 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 1pv7 chain A Region: 14 - 470 Aligned: 409 Modelled: 411 Confidence: 100.0% Identity: 10% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 3b9y chain A Region: 337 - 495 Aligned: 155 Modelled: 159 Confidence: 70.2% Identity: 7% 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 3hd6 chain A Region: 338 - 483 Aligned: 146 Modelled: 146 Confidence: 24.6% Identity: 12% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 2g9p chain A Region: 74 - 87 Aligned: 14 Modelled: 14 Confidence: 17.5% 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 2knc chain A Region: 427 - 473 Aligned: 47 Modelled: 47 Confidence: 9.2% Identity: 13% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3b60 chain A domain 2 Region: 11 - 85 Aligned: 75 Modelled: 75 Confidence: 7.3% Identity: 11% Fold: ABC transporter transmembrane region Superfamily: ABC transporter transmembrane region Family: ABC transporter transmembrane region Phyre2 PDB 3din chain D Region: 8 - 51 Aligned: 44 Modelled: 44 Confidence: 6.9% Identity: 9% PDB header:membrane protein, protein transport Chain: D: PDB Molecule:preprotein translocase subunit sece; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 3pro chain C domain 1 Region: 42 - 83 Aligned: 42 Modelled: 42 Confidence: 6.5% Identity: 12% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 PDB 3mk7 chain F Region: 433 - 483 Aligned: 51 Modelled: 51 Confidence: 6.4% Identity: 10% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 1 d1pw4a_ 2 c3o7pA_ 3 c2gfpA_ 4 c2xutC_ 5 d1pv7a_ 6 c3b9yA_ 7 c3hd6A_ 8 c2g9pA_ 9 c2kncA_ 10 d3b60a2 11 c3dinD_ 12 d3proc1 13 c3mk7F_

Detailed template information

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

1 d1pw4a_ 100.0 15 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 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) 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 c2xutC_ 100.0 9 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. 5 d1pv7a_ 100.0 10 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 6 c3b9yA_ 70.2 7 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 7 c3hd6A_ 24.6 12 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 8 c2g9pA_ 17.5 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 9 c2kncA_ 9.2 13 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 10 d3b60a2 7.3 11 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region 11 c3dinD_ 6.9 9 PDB header:membrane protein, protein transport Chain: D: PDB Molecule:preprotein translocase subunit sece; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase 12 d3proc1 6.5 12 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 13 c3mk7F_ 6.4 10 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase

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