Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	F	R	I	A	S	S	P	Y	T	H	N	Q	R	Q	T	S	R	I	M	L	L	V	L	L	A	A	V	P	G	I	A	A	Q	L	W	F	F	G	W	G	T	L	V	Q	I	L	L	A	S	V	S	A	L	L	A	E	A	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	L	K	L	R	K	Q	S	V	A	A	T	L	K	D	N	S	A	L	L	T	G	L	L	L	A	V	S	I	P	P	L	A	P	W	W	M	V	V	L	G	T	V	F	A	V	I	I	A	K	Q	L	Y	G	G	L	G	Q	N	P
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	N	P	A	M	I	G	Y	V	V	L	L	I	S	F	P	V	Q	M	T	S	W	L	P	P	H	E	I	A	V	N	I	P	G	F	I	D	A	I	Q	V	I	F	S	G	H	T	A	S	G	G	D	M	N	T	L	R	L	G	I
Secondary structure
SS confidence
Disorder																			?	?	?	?		?	?	?	?	?	?	?	?	?	?		?	?										?	?	?	?	?	?	?		?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		D	G	I	S	Q	A	T	P	L	D	T	F	K	T	S	V	R	A	G	H	S	V	E	Q	I	M	Q	Y	P	I	Y	S	G	I	L	A	G	A	G	W	Q	W	V	N	L	A	W	L	A	G	G	V	W	L	L	W	Q	K	A	I
Secondary structure
SS confidence
Disorder			?												?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		R	W	H	I	P	L	S	F	L	V	T	L	A	L	C	A	M	L	G	W	L	F	S	P	E	T	L	A	A	P	Q	I	H	L	L	S	G	A	T	M	L	G	A	F	F	I	L	T	D	P	V	T	A	S	T	T	N	R	G	R
Secondary structure
SS confidence
Disorder																																																					?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.
Sequence		L	I	F	G	A	L	A	G	L	L	V	W	L	I	R	S	F	G	G	Y	P	D	G	V	A	F	A	V	L	L	A	N	I	T	V	P	L	I	D	Y	Y	T	R	P	R	V	Y	G	H	R	K	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 3k3g chain A Region: 32 - 112 Aligned: 80 Modelled: 81 Confidence: 27.5% Identity: 24% PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea Phyre2 PDB 1iwg chain A domain 8 Region: 1 - 89 Aligned: 85 Modelled: 89 Confidence: 23.5% Identity: 9% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1oy8 chain A Region: 14 - 89 Aligned: 72 Modelled: 76 Confidence: 16.5% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump Phyre2 PDB 2knc chain A Region: 93 - 108 Aligned: 16 Modelled: 16 Confidence: 13.2% Identity: 25% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2l0e chain A Region: 279 - 292 Aligned: 14 Modelled: 14 Confidence: 11.4% Identity: 29% PDB header:membrane protein Chain: A: PDB Molecule:sodium/hydrogen exchanger 1; PDBTitle: structural and functional analysis of tm vi of the nhe1 isoform of the2 na+/h+ exchanger Phyre2 PDB 3knu chain D Region: 327 - 351 Aligned: 25 Modelled: 25 Confidence: 7.7% Identity: 24% PDB header:transferase Chain: D: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: crystal structure of trna (guanine-n1)-methyltransferase from2 anaplasma phagocytophilum Phyre2 PDB 1jb7 chain A domain 3 Region: 114 - 122 Aligned: 9 Modelled: 9 Confidence: 6.6% Identity: 67% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 1ymg chain A Region: 79 - 125 Aligned: 47 Modelled: 47 Confidence: 5.4% Identity: 21% PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution Phyre2 PDB 1ymg chain A domain 1 Region: 79 - 125 Aligned: 47 Modelled: 47 Confidence: 5.4% Identity: 21% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 2axt chain J domain 1 Region: 93 - 113 Aligned: 21 Modelled: 21 Confidence: 5.3% Identity: 29% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein J, PsbJ Family: PsbJ-like Phyre2 1 c3k3gA_ 2 d1iwga8 3 c1oy8A_ 4 c2kncA_ 5 c2l0eA_ 6 c3knuD_ 7 d1jb7a3 8 c1ymgA_ 9 d1ymga1 10 d2axtj1

Detailed template information

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

1 c3k3gA_ 27.5 24 PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea 2 d1iwga8 23.5 9 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 3 c1oy8A_ 16.5 13 PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump 4 c2kncA_ 13.2 25 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 5 c2l0eA_ 11.4 29 PDB header:membrane protein Chain: A: PDB Molecule:sodium/hydrogen exchanger 1; PDBTitle: structural and functional analysis of tm vi of the nhe1 isoform of the2 na+/h+ exchanger 6 c3knuD_ 7.7 24 PDB header:transferase Chain: D: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: crystal structure of trna (guanine-n1)-methyltransferase from2 anaplasma phagocytophilum 7 d1jb7a3 6.6 67 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 8 c1ymgA_ 5.4 21 PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution 9 d1ymga1 5.4 21 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 10 d2axtj1 5.3 29 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like

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