Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	F	K	T	N	K	L	S	L	N	L	V	L	A	S	S	L	L	A	A	S	I	P	A	F	A	V	T	G	D	T	D	Q	P	I	H	I	E	S	D	Q	Q	S	L	D	M	Q	G	N	V	V	T	F	T	G	N	V	I	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	Q	G	T	I	K	I	N	A	D	K	V	V	V	T	R	P	G	G	E	Q	G	K	E	V	I	D	G	Y	G	K	P	A	T	F	Y	Q	M	Q	D	N	G	K	P	V	E	G	H	A	S	Q	M	H	Y	E	L	A	K	D	F
Secondary structure
SS confidence
Disorder																				?		?		?																	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	V	L	T	G	N	A	Y	L	Q	Q	V	D	S	N	I	K	G	D	K	I	T	Y	L	V	K	E	Q	K	M	Q	A	F	S	D	K	G	K	R	V	T	T	V	L	V	P	S	Q	L	Q	D	K	N	N	K	G	Q	T	P	A
Secondary structure
SS confidence
Disorder													?	?	?													?	?						?	?	?	?	?									?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.
Sequence		Q	K	K	G	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 2r1a chain D Region: 28 - 166 Aligned: 136 Modelled: 139 Confidence: 100.0% Identity: 99% PDB header:transport protein Chain: D: PDB Molecule:protein yhbn; PDBTitle: crystal structure of the periplasmic lipopolysaccharide transport2 protein lpta (yhbn), trigonal form Phyre2 PDB 3my2 chain A Region: 37 - 165 Aligned: 118 Modelled: 129 Confidence: 98.8% Identity: 19% PDB header:transport protein Chain: A: PDB Molecule:lipopolysaccharide export system protein lptc; PDBTitle: crystal structure of lptc Phyre2 PDB 1g7s chain A domain 1 Region: 145 - 174 Aligned: 30 Modelled: 30 Confidence: 25.0% Identity: 17% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Elongation factors Phyre2 PDB 1ueb chain A domain 3 Region: 118 - 151 Aligned: 34 Modelled: 34 Confidence: 8.6% Identity: 15% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1xct chain L Region: 29 - 56 Aligned: 28 Modelled: 28 Confidence: 7.2% Identity: 14% PDB header:immune system Chain: L: PDB Molecule:protein l; PDBTitle: complex hcv core-fab 19d9d6-protein l mutant (d55a, l57h, y64w) in2 space group p21212 Phyre2 PDB 2ptl chain A Region: 31 - 56 Aligned: 26 Modelled: 26 Confidence: 7.1% Identity: 15% Fold: beta-Grasp (ubiquitin-like) Superfamily: Immunoglobulin-binding domains Family: Immunoglobulin-binding domains Phyre2 PDB 2jmb chain A Region: 111 - 148 Aligned: 38 Modelled: 38 Confidence: 6.8% Identity: 16% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein atu4866; PDBTitle: solution structure of the protein atu4866 from agrobacterium2 tumefaciens Phyre2 1 c2r1aD_ 2 c3my2A_ 3 d1g7sa1 4 d1ueba3 5 c1xctL_ 6 d2ptla_ 7 c2jmbA_

Detailed template information

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

1 c2r1aD_ 100.0 99 PDB header:transport protein Chain: D: PDB Molecule:protein yhbn; PDBTitle: crystal structure of the periplasmic lipopolysaccharide transport2 protein lpta (yhbn), trigonal form 2 c3my2A_ 98.8 19 PDB header:transport protein Chain: A: PDB Molecule:lipopolysaccharide export system protein lptc; PDBTitle: crystal structure of lptc 3 d1g7sa1 25.0 17 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 4 d1ueba3 8.6 15 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 5 c1xctL_ 7.2 14 PDB header:immune system Chain: L: PDB Molecule:protein l; PDBTitle: complex hcv core-fab 19d9d6-protein l mutant (d55a, l57h, y64w) in2 space group p21212 6 d2ptla_ 7.1 15 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 7 c2jmbA_ 6.8 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein atu4866; PDBTitle: solution structure of the protein atu4866 from agrobacterium2 tumefaciens

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