Secondary structure and disorder prediction

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Sequence		M	N	I	E	N	L	K	T	K	A	E	A	D	I	S	E	Y	I	T	K	K	I	I	E	L	K	K	K	T	G	K	E	V	T	S	I	Q	F	T	A	R	E	K	M	T	G	L	E	S	Y	D	V	K	I	N	L	I
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 1avo chain A Region: 4 - 25 Aligned: 22 Modelled: 22 Confidence: 33.6% Identity: 50% PDB header:proteasome activator Chain: A: PDB Molecule:11s regulator; PDBTitle: proteasome activator reg(alpha) Phyre2 PDB 1div chain A domain 1 Region: 19 - 56 Aligned: 38 Modelled: 38 Confidence: 23.1% Identity: 21% Fold: Ribosomal protein L9 C-domain Superfamily: Ribosomal protein L9 C-domain Family: Ribosomal protein L9 C-domain Phyre2 PDB 1rep chain C domain 2 Region: 28 - 43 Aligned: 16 Modelled: 16 Confidence: 13.0% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Replication initiation protein Phyre2 PDB 1uww chain A Region: 36 - 56 Aligned: 21 Modelled: 21 Confidence: 10.8% Identity: 48% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 28 carbohydrate binding module, CBM28 Phyre2 PDB 2z9o chain B Region: 28 - 45 Aligned: 18 Modelled: 18 Confidence: 9.2% Identity: 33% PDB header:replication/dna Chain: B: PDB Molecule:replication initiation protein; PDBTitle: crystal structure of the dimeric form of repe in complex with the repe2 operator dna Phyre2 PDB 2kvt chain A Region: 26 - 40 Aligned: 15 Modelled: 15 Confidence: 9.0% Identity: 47% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yaia; PDBTitle: solution nmr structure of yaia from escherichia eoli. northeast2 structural genomics target er244 Phyre2 PDB 2nra chain C domain 2 Region: 27 - 39 Aligned: 13 Modelled: 13 Confidence: 8.8% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Replication initiation protein Phyre2 PDB 2nra chain C Region: 28 - 43 Aligned: 16 Modelled: 16 Confidence: 7.9% Identity: 19% PDB header:replication/dna Chain: C: PDB Molecule:pi protein; PDBTitle: crystal structure of pi initiator protein in complex with iteron dna Phyre2 PDB 2j01 chain I domain 1 Region: 19 - 56 Aligned: 38 Modelled: 38 Confidence: 7.8% Identity: 16% Fold: Ribosomal protein L9 C-domain Superfamily: Ribosomal protein L9 C-domain Family: Ribosomal protein L9 C-domain Phyre2 1 c1avoA_ 2 d1diva1 3 d1repc2 4 d1uwwa_ 5 c2z9oB_ 6 c2kvtA_ 7 d2nrac2 8 c2nraC_ 9 d2j01i1

Detailed template information

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

1 c1avoA_ 33.6 50 PDB header:proteasome activator Chain: A: PDB Molecule:11s regulator; PDBTitle: proteasome activator reg(alpha) 2 d1diva1 23.1 21 Fold:Ribosomal protein L9 C-domain Superfamily:Ribosomal protein L9 C-domain Family:Ribosomal protein L9 C-domain 3 d1repc2 13.0 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 4 d1uwwa_ 10.8 48 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 28 carbohydrate binding module, CBM28 5 c2z9oB_ 9.2 33 PDB header:replication/dna Chain: B: PDB Molecule:replication initiation protein; PDBTitle: crystal structure of the dimeric form of repe in complex with the repe2 operator dna 6 c2kvtA_ 9.0 47 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yaia; PDBTitle: solution nmr structure of yaia from escherichia eoli. northeast2 structural genomics target er244 7 d2nrac2 8.8 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 8 c2nraC_ 7.9 19 PDB header:replication/dna Chain: C: PDB Molecule:pi protein; PDBTitle: crystal structure of pi initiator protein in complex with iteron dna 9 d2j01i1 7.8 16 Fold:Ribosomal protein L9 C-domain Superfamily:Ribosomal protein L9 C-domain Family:Ribosomal protein L9 C-domain

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