Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	K	D	E	A	G	G	N	W	K	Q	F	K	G	K	V	K	E	Q	W	G	K	L	T	D	D	D	M	T	I	I	E	G	K	R	D	Q	L	V	G	K	I	Q	E	R	Y	G	Y	Q	K	D	Q	A	E	K	E	V	V	D
Secondary structure
SS confidence
Disorder		?	?					?																										?																?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		W	E	T	R	N	E	Y	R	W
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 1ryk chain A Region: 1 - 69 Aligned: 69 Modelled: 69 Confidence: 100.0% Identity: 100% Fold: SAM domain-like Superfamily: Hypothetical protein YjbJ Family: Hypothetical protein YjbJ Phyre2 PDB 1yww chain A Region: 1 - 64 Aligned: 64 Modelled: 64 Confidence: 99.9% Identity: 55% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa4738; PDBTitle: nmr structure of p. aeruginosa protein pa4738: northeast2 structural genomics consortium target pap2 Phyre2 PDB 2l9q chain A Region: 3 - 66 Aligned: 64 Modelled: 64 Confidence: 16.1% Identity: 19% PDB header:chaperone Chain: A: PDB Molecule:12 kda heat shock protein; PDBTitle: structural characterization of small heat shock protein (hsp12) Phyre2 PDB 2js5 chain B Region: 37 - 67 Aligned: 31 Modelled: 31 Confidence: 9.8% Identity: 16% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q60c73_metca. northeast structural2 genomics consortium target mcr1 Phyre2 PDB 2k88 chain A Region: 29 - 66 Aligned: 38 Modelled: 38 Confidence: 8.4% Identity: 21% PDB header:hydrolase Chain: A: PDB Molecule:vacuolar proton pump subunit g; PDBTitle: association of subunit d (vma6p) and e (vma4p) with g2 (vma10p) and the nmr solution structure of subunit g (g1-3 59) of the saccharomyces cerevisiae v1vo atpase Phyre2 PDB 3lf9 chain A Region: 22 - 67 Aligned: 46 Modelled: 46 Confidence: 5.7% Identity: 11% PDB header:immune system Chain: A: PDB Molecule:4e10_d0_1is1a_001_c (t161); PDBTitle: crystal structure of hiv epitope-scaffold 4e10_d0_1is1a_001_c Phyre2 1 d1ryka_ 2 c1ywwA_ 3 c2l9qA_ 4 c2js5B_ 5 c2k88A_ 6 c3lf9A_

Detailed template information

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

1 d1ryka_ 100.0 100 Fold:SAM domain-like Superfamily:Hypothetical protein YjbJ Family:Hypothetical protein YjbJ 2 c1ywwA_ 99.9 55 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa4738; PDBTitle: nmr structure of p. aeruginosa protein pa4738: northeast2 structural genomics consortium target pap2 3 c2l9qA_ 16.1 19 PDB header:chaperone Chain: A: PDB Molecule:12 kda heat shock protein; PDBTitle: structural characterization of small heat shock protein (hsp12) 4 c2js5B_ 9.8 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q60c73_metca. northeast structural2 genomics consortium target mcr1 5 c2k88A_ 8.4 21 PDB header:hydrolase Chain: A: PDB Molecule:vacuolar proton pump subunit g; PDBTitle: association of subunit d (vma6p) and e (vma4p) with g2 (vma10p) and the nmr solution structure of subunit g (g1-3 59) of the saccharomyces cerevisiae v1vo atpase 6 c3lf9A_ 5.7 11 PDB header:immune system Chain: A: PDB Molecule:4e10_d0_1is1a_001_c (t161); PDBTitle: crystal structure of hiv epitope-scaffold 4e10_d0_1is1a_001_c

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