Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	K	K	F	I	A	P	L	L	A	L	L	V	S	G	C	Q	I	D	P	Y	T	H	A	P	T	L	T	S	T	D	W	Y	D	V	G	M	E	D	A	I	S	G	S	A	I	K	D	D	D	A	F	S	D	S	Q	A	D	R
Secondary structure
SS confidence
Disorder		?	?															?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?												?	?			?	?					?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	L	Y	L	K	G	Y	A	E	G	Q	K	K	T	C	Q	T	D	F	T	Y	A	R	G	L	S	G	K	S	F	P	A	S	C	N	N	V	E	N	A	S	Q	L	H	E	V	W	Q	K	G	A	D	E	N	A	S	T	I	R	L
Secondary structure
SS confidence
Disorder																											?				?	?	?	?	?	?			?	?														?	?	?	?	?	?	?	?
Disorder confidence
		.
Sequence		N
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 2jrm chain A Region: 34 - 74 Aligned: 39 Modelled: 41 Confidence: 68.1% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55 Phyre2 PDB 2ae3 chain A Region: 44 - 74 Aligned: 31 Modelled: 31 Confidence: 11.9% Identity: 16% PDB header:hydrolase Chain: A: PDB Molecule:glutaryl 7-aminocephalosporanic acid acylase; PDBTitle: glutaryl 7-aminocephalosporanic acid acylase: mutational study of2 activation mechanism Phyre2 PDB 2khg chain A Region: 37 - 49 Aligned: 13 Modelled: 13 Confidence: 7.5% Identity: 38% PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in tfe Phyre2 PDB 2ijr chain A domain 1 Region: 3 - 30 Aligned: 26 Modelled: 26 Confidence: 6.8% Identity: 15% Fold: Api92-like Superfamily: Api92-like Family: Api92-like Phyre2 PDB 2wyb chain A Region: 44 - 74 Aligned: 31 Modelled: 31 Confidence: 6.0% Identity: 16% PDB header:hydrolase Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid Phyre2 PDB 2fxt chain A domain 1 Region: 60 - 82 Aligned: 22 Modelled: 23 Confidence: 5.6% Identity: 23% Fold: Cystatin-like Superfamily: NTF2-like Family: TIM44-like Phyre2 1 c2jrmA_ 2 c2ae3A_ 3 c2khgA_ 4 d2ijra1 5 c2wybA_ 6 d2fxta1

Detailed template information

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

1 c2jrmA_ 68.1 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55 2 c2ae3A_ 11.9 16 PDB header:hydrolase Chain: A: PDB Molecule:glutaryl 7-aminocephalosporanic acid acylase; PDBTitle: glutaryl 7-aminocephalosporanic acid acylase: mutational study of2 activation mechanism 3 c2khgA_ 7.5 38 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in tfe 4 d2ijra1 6.8 15 Fold:Api92-like Superfamily:Api92-like Family:Api92-like 5 c2wybA_ 6.0 16 PDB header:hydrolase Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid 6 d2fxta1 5.6 23 Fold:Cystatin-like Superfamily:NTF2-like Family:TIM44-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