Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	E	A	L	S	L	F	S	L	F	A	S	S	F	L	S	A	T	L	L	P	G	N	S	E	V	V	L	V	A	M	L	L	S	G	I	S	H	P	W	V	L	V	L	T	A	T	M	G	N	S	L	G	G	L	T	N	V	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?														?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	G	R	F	F	P	L	R	K	T	S	R	W	Q	E	K	A	T	G	W	L	K	R	Y	G	A	V	T	L	L	L	S	W	M	P	V	V	G	D	L	L	C	L	L	A	G	W	M	R	I	S	W	G	P	V	I	F	F	L	C
Secondary structure
SS confidence
Disorder										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.
Sequence		L	G	K	A	L	R	Y	V	A	V	A	A	A	T	V	Q	G	M	M	W	W	H
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 2oso chain A domain 1 Region: 55 - 86 Aligned: 32 Modelled: 29 Confidence: 49.7% Identity: 13% Fold: Ligand-binding domain in the NO signalling and Golgi transport Superfamily: Ligand-binding domain in the NO signalling and Golgi transport Family: MJ1460-like Phyre2 PDB 1w6k chain A domain 2 Region: 50 - 88 Aligned: 39 Modelled: 39 Confidence: 48.9% Identity: 15% Fold: alpha/alpha toroid Superfamily: Terpenoid cyclases/Protein prenyltransferases Family: Terpene synthases Phyre2 PDB 3njc chain A Region: 55 - 86 Aligned: 32 Modelled: 28 Confidence: 30.8% Identity: 9% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:yslb protein; PDBTitle: crystal structure of the yslb protein from bacillus subtilis.2 northeast structural genomics consortium target sr460. Phyre2 PDB 1p58 chain F Region: 72 - 94 Aligned: 23 Modelled: 23 Confidence: 23.3% Identity: 13% PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction Phyre2 PDB 2hnh chain A Region: 50 - 114 Aligned: 65 Modelled: 65 Confidence: 12.2% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:dna polymerase iii alpha subunit; PDBTitle: crystal structure of the catalytic alpha subunit of e. coli2 replicative dna polymerase iii Phyre2 PDB 3e0d chain A Region: 50 - 114 Aligned: 65 Modelled: 65 Confidence: 11.5% Identity: 23% PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase iii subunit alpha; PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit Phyre2 PDB 1w6k chain A Region: 50 - 88 Aligned: 39 Modelled: 39 Confidence: 11.2% Identity: 15% PDB header:isomerase Chain: A: PDB Molecule:lanosterol synthase; PDBTitle: structure of human osc in complex with lanosterol Phyre2 PDB 2csb chain A domain 4 Region: 75 - 88 Aligned: 14 Modelled: 14 Confidence: 10.6% Identity: 43% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Topoisomerase V repeat domain Phyre2 PDB 2lbg chain A Region: 46 - 67 Aligned: 22 Modelled: 22 Confidence: 8.3% Identity: 32% PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles Phyre2 1 d2osoa1 2 d1w6ka2 3 c3njcA_ 4 c1p58F_ 5 c2hnhA_ 6 c3e0dA_ 7 c1w6kA_ 8 d2csba4 9 c2lbgA_

Detailed template information

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

1 d2osoa1 49.7 13 Fold:Ligand-binding domain in the NO signalling and Golgi transport Superfamily:Ligand-binding domain in the NO signalling and Golgi transport Family:MJ1460-like 2 d1w6ka2 48.9 15 Fold:alpha/alpha toroid Superfamily:Terpenoid cyclases/Protein prenyltransferases Family:Terpene synthases 3 c3njcA_ 30.8 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:yslb protein; PDBTitle: crystal structure of the yslb protein from bacillus subtilis.2 northeast structural genomics consortium target sr460. 4 c1p58F_ 23.3 13 PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 5 c2hnhA_ 12.2 14 PDB header:transferase Chain: A: PDB Molecule:dna polymerase iii alpha subunit; PDBTitle: crystal structure of the catalytic alpha subunit of e. coli2 replicative dna polymerase iii 6 c3e0dA_ 11.5 23 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase iii subunit alpha; PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit 7 c1w6kA_ 11.2 15 PDB header:isomerase Chain: A: PDB Molecule:lanosterol synthase; PDBTitle: structure of human osc in complex with lanosterol 8 d2csba4 10.6 43 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Topoisomerase V repeat domain 9 c2lbgA_ 8.3 32 PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles

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