Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	G	K	N	K	F	N	T	Y	V	V	S	F	D	Y	P	S	S	Y	S	S	V	F	L	R	L	R	S	L	M	Y	D	M	N	F	S	S	I	V	A	D	E	Y	G	I	P	R	Q	L	N	E	N	S	F	A	I	T	T	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?		?																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.
Sequence		L	A	A	S	E	I	E	D	L	I	R	L	K	C	L	D	L	P	D	I	D	F	D	L	N	I	M	T	V	D	D	Y	F	R	Q	F	Y	K
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 2rk5 chain A domain 1 Region: 48 - 83 Aligned: 33 Modelled: 36 Confidence: 18.6% Identity: 15% Fold: FAD-binding/transporter-associated domain-like Superfamily: FAD-binding/transporter-associated domain-like Family: CorC/HlyC domain-like Phyre2 PDB 1t2s chain A Region: 87 - 98 Aligned: 11 Modelled: 12 Confidence: 12.7% Identity: 27% Fold: SH3-like barrel Superfamily: PAZ domain Family: PAZ domain Phyre2 PDB 1r6z chain A domain 1 Region: 87 - 98 Aligned: 12 Modelled: 12 Confidence: 11.2% Identity: 25% Fold: SH3-like barrel Superfamily: PAZ domain Family: PAZ domain Phyre2 PDB 2be6 chain F Region: 89 - 96 Aligned: 8 Modelled: 8 Confidence: 9.8% Identity: 50% PDB header:membrane protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel alpha-1c subunit; PDBTitle: 2.0 a crystal structure of the cav1.2 iq domain-ca/cam complex Phyre2 PDB 3fqi chain A Region: 71 - 85 Aligned: 15 Modelled: 15 Confidence: 9.6% Identity: 40% PDB header:protein binding Chain: A: PDB Molecule:protein dom3z; PDBTitle: crystal structure of the mouse dom3z Phyre2 PDB 1nw3 chain A Region: 62 - 82 Aligned: 21 Modelled: 21 Confidence: 9.0% Identity: 43% Fold: S-adenosyl-L-methionine-dependent methyltransferases Superfamily: S-adenosyl-L-methionine-dependent methyltransferases Family: Catalytic, N-terminal domain of histone methyltransferase Dot1l Phyre2 PDB 1nw3 chain A Region: 62 - 82 Aligned: 21 Modelled: 21 Confidence: 9.0% Identity: 43% PDB header:transferase Chain: A: PDB Molecule:histone methyltransferase dot1l; PDBTitle: structure of the catalytic domain of human dot1l, a non-set2 domain nucleosomal histone methyltransferase Phyre2 PDB 1si2 chain A Region: 87 - 98 Aligned: 12 Modelled: 12 Confidence: 8.1% Identity: 50% Fold: SH3-like barrel Superfamily: PAZ domain Family: PAZ domain Phyre2 PDB 1h6z chain A domain 2 Region: 34 - 47 Aligned: 14 Modelled: 14 Confidence: 7.8% Identity: 21% Fold: The "swivelling" beta/beta/alpha domain Superfamily: Phosphohistidine domain Family: Pyruvate phosphate dikinase, central domain Phyre2 PDB 2b0l chain A domain 1 Region: 37 - 48 Aligned: 12 Modelled: 12 Confidence: 7.5% Identity: 50% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: CodY HTH domain Phyre2 PDB 2k9q chain B Region: 40 - 77 Aligned: 38 Modelled: 38 Confidence: 7.5% Identity: 34% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of hth_xre family transcriptional2 regulator bt_p548217 from bacteroides thetaiotaomicron.3 northeast structural genomics consortium target btr244. Phyre2 PDB 3m1c chain B Region: 60 - 78 Aligned: 19 Modelled: 19 Confidence: 7.5% Identity: 37% PDB header:viral protein Chain: B: PDB Molecule:envelope glycoprotein l; PDBTitle: crystal structure of the conserved herpesvirus fusion regulator2 complex gh-gl Phyre2 PDB 1bw6 chain A Region: 40 - 48 Aligned: 9 Modelled: 9 Confidence: 7.3% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 1hlv chain A domain 1 Region: 40 - 49 Aligned: 10 Modelled: 10 Confidence: 7.3% Identity: 30% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 1kbl chain A domain 2 Region: 34 - 47 Aligned: 14 Modelled: 14 Confidence: 7.3% Identity: 21% Fold: The "swivelling" beta/beta/alpha domain Superfamily: Phosphohistidine domain Family: Pyruvate phosphate dikinase, central domain Phyre2 PDB 2fc7 chain A domain 1 Region: 70 - 84 Aligned: 15 Modelled: 15 Confidence: 7.3% Identity: 33% Fold: RING/U-box Superfamily: RING/U-box Family: ZZ domain Phyre2 PDB 3kow chain H Region: 28 - 41 Aligned: 14 Modelled: 14 Confidence: 7.3% Identity: 50% PDB header:metal binding protein Chain: H: PDB Molecule:d-ornithine aminomutase s component; PDBTitle: crystal structure of ornithine 4,5 aminomutase backsoaked complex Phyre2 PDB 3zrg chain B Region: 87 - 92 Aligned: 6 Modelled: 6 Confidence: 7.3% Identity: 100% PDB header:protein binding Chain: B: PDB Molecule:pexrd2 family secreted rxlr effector peptide, putative; PDBTitle: crystal structure of rxlr effector pexrd2 from phytophthora infestans Phyre2 PDB 1q8i chain A domain 2 Region: 1 - 73 Aligned: 68 Modelled: 73 Confidence: 7.1% Identity: 13% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: DNA polymerase I Phyre2 PDB 1kke chain A domain 2 Region: 83 - 92 Aligned: 10 Modelled: 10 Confidence: 7.0% Identity: 50% Fold: Virus attachment protein globular domain Superfamily: Virus attachment protein globular domain Family: Reovirus attachment protein sigma 1 head domain Phyre2 1 d2rk5a1 2 d1t2sa_ 3 d1r6za1 4 c2be6F_ 5 c3fqiA_ 6 d1nw3a_ 7 c1nw3A_ 8 d1si2a_ 9 d1h6za2 10 d2b0la1 11 c2k9qB_ 12 c3m1cB_ 13 d1bw6a_ 14 d1hlva1 15 d1kbla2 16 d2fc7a1 17 c3kowH_ 18 c3zrgB_ 19 d1q8ia2 20 d1kkea2 21 22 23 24 25 26 27 28

Detailed template information

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

1 d2rk5a1 18.6 15 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:CorC/HlyC domain-like 2 d1t2sa_ 12.7 27 Fold:SH3-like barrel Superfamily:PAZ domain Family:PAZ domain 3 d1r6za1 11.2 25 Fold:SH3-like barrel Superfamily:PAZ domain Family:PAZ domain 4 c2be6F_ 9.8 50 PDB header:membrane protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel alpha-1c subunit; PDBTitle: 2.0 a crystal structure of the cav1.2 iq domain-ca/cam complex 5 c3fqiA_ 9.6 40 PDB header:protein binding Chain: A: PDB Molecule:protein dom3z; PDBTitle: crystal structure of the mouse dom3z 6 d1nw3a_ 9.0 43 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Catalytic, N-terminal domain of histone methyltransferase Dot1l 7 c1nw3A_ 9.0 43 PDB header:transferase Chain: A: PDB Molecule:histone methyltransferase dot1l; PDBTitle: structure of the catalytic domain of human dot1l, a non-set2 domain nucleosomal histone methyltransferase 8 d1si2a_ 8.1 50 Fold:SH3-like barrel Superfamily:PAZ domain Family:PAZ domain 9 d1h6za2 7.8 21 Fold:The "swivelling" beta/beta/alpha domain Superfamily:Phosphohistidine domain Family:Pyruvate phosphate dikinase, central domain 10 d2b0la1 7.5 50 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CodY HTH domain 11 c2k9qB_ 7.5 34 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of hth_xre family transcriptional2 regulator bt_p548217 from bacteroides thetaiotaomicron.3 northeast structural genomics consortium target btr244. 12 c3m1cB_ 7.5 37 PDB header:viral protein Chain: B: PDB Molecule:envelope glycoprotein l; PDBTitle: crystal structure of the conserved herpesvirus fusion regulator2 complex gh-gl 13 d1bw6a_ 7.3 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 14 d1hlva1 7.3 30 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 15 d1kbla2 7.3 21 Fold:The "swivelling" beta/beta/alpha domain Superfamily:Phosphohistidine domain Family:Pyruvate phosphate dikinase, central domain 16 d2fc7a1 7.3 33 Fold:RING/U-box Superfamily:RING/U-box Family:ZZ domain 17 c3kowH_ 7.3 50 PDB header:metal binding protein Chain: H: PDB Molecule:d-ornithine aminomutase s component; PDBTitle: crystal structure of ornithine 4,5 aminomutase backsoaked complex 18 c3zrgB_ 7.3 100 PDB header:protein binding Chain: B: PDB Molecule:pexrd2 family secreted rxlr effector peptide, putative; PDBTitle: crystal structure of rxlr effector pexrd2 from phytophthora infestans 19 d1q8ia2 7.1 13 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:DNA polymerase I 20 d1kkea2 7.0 50 Fold:Virus attachment protein globular domain Superfamily:Virus attachment protein globular domain Family:Reovirus attachment protein sigma 1 head domain 21 d2ghvc1 not modelled 6.9 25 Fold:SARS receptor-binding domain-like Superfamily:SARS receptor-binding domain-like Family:SARS receptor-binding domain-like 22 c2elhA_ not modelled 6.4 33 PDB header:dna binding protein Chain: A: PDB Molecule:cg11849-pa; PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa 23 d2coba1 not modelled 6.1 44 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 24 d2dloa2 not modelled 5.9 29 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 25 d1s5ja2 not modelled 5.7 15 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:DNA polymerase I 26 d1vbga2 not modelled 5.7 25 Fold:The "swivelling" beta/beta/alpha domain Superfamily:Phosphohistidine domain Family:Pyruvate phosphate dikinase, central domain 27 c1kkeA_ not modelled 5.3 50 PDB header:viral protein Chain: A: PDB Molecule:sigma 1 protein; PDBTitle: crystal structure of reovirus attachment protein sigma12 trimer 28 c3o7vX_ not modelled 5.1 25 PDB header:rna binding protein/rna Chain: X: PDB Molecule:piwi-like protein 1; PDBTitle: crystal structure of human hiwi1 (v361m) paz domain (residues 277-399)2 in complex with 14-mer rna (12-bp + 2-nt overhang) containing 2'-och33 at its 3'-end

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