Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	P	L	E	R	I	T	Q	L	V	N	I	N	G	D	V	N	N	P	D	T	P	R	P	L	L	S	L	E	D	F	F	I	D	N	N	I	H	G	S	I	C	C	N	V	I	P	E	Q	S	P	Q	A	I	Y	H	H	F	L
Secondary structure
SS confidence
Disorder		?	?	?													?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	I	R	E	R	N	N	V	S	D	V	L	V	E	I	T	M	F	D	D	P	D	W	P	F	S	E	S	I	L	V	I	T	T	A	S	P	E	E	V	Q	S	W	F	V	E	E	I	A	P	D	E	C	W	E	G	W	S	E	D
Secondary structure
SS confidence
Disorder					?				?																																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140
Sequence		T	E	H	G	W	V	E	V	P	V	G	M	H	P	V	T	C	W	W	D
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 1yg2 chain A Region: 49 - 111 Aligned: 48 Modelled: 48 Confidence: 61.0% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: PadR-like Phyre2 PDB 3l9f chain D Region: 49 - 113 Aligned: 59 Modelled: 65 Confidence: 55.0% Identity: 15% PDB header:transcription regulator Chain: D: PDB Molecule:putative uncharacterized protein smu.1604c; PDBTitle: the crystal structure of smu.1604c from streptococcus mutans ua159 Phyre2 PDB 2gjv chain A domain 1 Region: 15 - 38 Aligned: 24 Modelled: 24 Confidence: 25.8% Identity: 29% Fold: Phage tail protein-like Superfamily: Phage tail protein-like Family: STM4215-like Phyre2 PDB 2gjv chain F Region: 15 - 38 Aligned: 24 Modelled: 24 Confidence: 25.6% Identity: 29% PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative cytoplasmic protein; PDBTitle: crystal structure of a protein of unknown function from salmonella2 typhimurium Phyre2 PDB 2esh chain A domain 1 Region: 49 - 104 Aligned: 45 Modelled: 56 Confidence: 22.9% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: PadR-like Phyre2 PDB 1mjd chain A Region: 4 - 35 Aligned: 32 Modelled: 32 Confidence: 19.3% Identity: 25% Fold: beta-Grasp (ubiquitin-like) Superfamily: Doublecortin (DC) Family: Doublecortin (DC) Phyre2 PDB 2dt7 chain A Region: 53 - 64 Aligned: 12 Modelled: 12 Confidence: 14.9% Identity: 25% PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor 3a subunit 3; PDBTitle: solution structure of the second surp domain of human2 splicing factor sf3a120 in complex with a fragment of3 human splicing factor sf3a60 Phyre2 PDB 1y4o chain A domain 1 Region: 53 - 73 Aligned: 21 Modelled: 21 Confidence: 14.4% Identity: 10% Fold: Profilin-like Superfamily: Roadblock/LC7 domain Family: Roadblock/LC7 domain Phyre2 PDB 3abf chain B Region: 52 - 88 Aligned: 36 Modelled: 37 Confidence: 12.6% Identity: 14% PDB header:isomerase Chain: B: PDB Molecule:4-oxalocrotonate tautomerase; PDBTitle: crystal structure of a 4-oxalocrotonate tautomerase homologue2 (tthb242) Phyre2 PDB 1mg4 chain A Region: 4 - 35 Aligned: 32 Modelled: 32 Confidence: 11.7% Identity: 25% Fold: beta-Grasp (ubiquitin-like) Superfamily: Doublecortin (DC) Family: Doublecortin (DC) Phyre2 PDB 2nu7 chain B domain 1 Region: 44 - 76 Aligned: 33 Modelled: 33 Confidence: 11.1% Identity: 24% Fold: Flavodoxin-like Superfamily: Succinyl-CoA synthetase domains Family: Succinyl-CoA synthetase domains Phyre2 PDB 1uf0 chain A Region: 4 - 35 Aligned: 32 Modelled: 32 Confidence: 9.7% Identity: 25% Fold: beta-Grasp (ubiquitin-like) Superfamily: Doublecortin (DC) Family: Doublecortin (DC) Phyre2 PDB 1euc chain B domain 1 Region: 44 - 76 Aligned: 33 Modelled: 33 Confidence: 8.9% Identity: 18% Fold: Flavodoxin-like Superfamily: Succinyl-CoA synthetase domains Family: Succinyl-CoA synthetase domains Phyre2 PDB 2o3b chain B domain 1 Region: 19 - 33 Aligned: 15 Modelled: 15 Confidence: 8.5% Identity: 27% Fold: Nuclease A inhibitor (NuiA) Superfamily: Nuclease A inhibitor (NuiA) Family: Nuclease A inhibitor (NuiA) Phyre2 PDB 2oqe chain A domain 1 Region: 14 - 84 Aligned: 49 Modelled: 49 Confidence: 8.5% Identity: 22% Fold: Supersandwich Superfamily: Amine oxidase catalytic domain Family: Amine oxidase catalytic domain Phyre2 PDB 1zcc chain A domain 1 Region: 3 - 34 Aligned: 31 Modelled: 32 Confidence: 7.8% Identity: 13% Fold: TIM beta/alpha-barrel Superfamily: PLC-like phosphodiesterases Family: Glycerophosphoryl diester phosphodiesterase Phyre2 PDB 1tz9 chain A Region: 58 - 87 Aligned: 30 Modelled: 30 Confidence: 7.7% Identity: 20% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: UxuA-like Phyre2 PDB 1o4y chain A Region: 123 - 140 Aligned: 18 Modelled: 18 Confidence: 7.7% Identity: 28% Fold: Concanavalin A-like lectins/glucanases Superfamily: Concanavalin A-like lectins/glucanases Family: Glycosyl hydrolases family 16 Phyre2 PDB 2dnf chain A Region: 4 - 35 Aligned: 32 Modelled: 32 Confidence: 7.5% Identity: 16% PDB header:protein binding Chain: A: PDB Molecule:doublecortin domain-containing protein 2; PDBTitle: solution structure of rsgi ruh-062, a dcx domain from human Phyre2 PDB 3elk chain A Region: 49 - 103 Aligned: 48 Modelled: 55 Confidence: 7.3% Identity: 17% PDB header:transcription regulator Chain: A: PDB Molecule:putative transcriptional regulator ta0346; PDBTitle: crystal structure of putative transcriptional regulator ta0346 from2 thermoplasma acidophilum Phyre2 1 d1yg2a_ 2 c3l9fD_ 3 d2gjva1 4 c2gjvF_ 5 d2esha1 6 d1mjda_ 7 c2dt7A_ 8 d1y4oa1 9 c3abfB_ 10 d1mg4a_ 11 d2nu7b1 12 d1uf0a_ 13 d1eucb1 14 d2o3bb1 15 d2oqea1 16 d1zcca1 17 d1tz9a_ 18 d1o4ya_ 19 c2dnfA_ 20 c3elkA_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 d1yg2a_ 61.0 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PadR-like 2 c3l9fD_ 55.0 15 PDB header:transcription regulator Chain: D: PDB Molecule:putative uncharacterized protein smu.1604c; PDBTitle: the crystal structure of smu.1604c from streptococcus mutans ua159 3 d2gjva1 25.8 29 Fold:Phage tail protein-like Superfamily:Phage tail protein-like Family:STM4215-like 4 c2gjvF_ 25.6 29 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative cytoplasmic protein; PDBTitle: crystal structure of a protein of unknown function from salmonella2 typhimurium 5 d2esha1 22.9 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PadR-like 6 d1mjda_ 19.3 25 Fold:beta-Grasp (ubiquitin-like) Superfamily:Doublecortin (DC) Family:Doublecortin (DC) 7 c2dt7A_ 14.9 25 PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor 3a subunit 3; PDBTitle: solution structure of the second surp domain of human2 splicing factor sf3a120 in complex with a fragment of3 human splicing factor sf3a60 8 d1y4oa1 14.4 10 Fold:Profilin-like Superfamily:Roadblock/LC7 domain Family:Roadblock/LC7 domain 9 c3abfB_ 12.6 14 PDB header:isomerase Chain: B: PDB Molecule:4-oxalocrotonate tautomerase; PDBTitle: crystal structure of a 4-oxalocrotonate tautomerase homologue2 (tthb242) 10 d1mg4a_ 11.7 25 Fold:beta-Grasp (ubiquitin-like) Superfamily:Doublecortin (DC) Family:Doublecortin (DC) 11 d2nu7b1 11.1 24 Fold:Flavodoxin-like Superfamily:Succinyl-CoA synthetase domains Family:Succinyl-CoA synthetase domains 12 d1uf0a_ 9.7 25 Fold:beta-Grasp (ubiquitin-like) Superfamily:Doublecortin (DC) Family:Doublecortin (DC) 13 d1eucb1 8.9 18 Fold:Flavodoxin-like Superfamily:Succinyl-CoA synthetase domains Family:Succinyl-CoA synthetase domains 14 d2o3bb1 8.5 27 Fold:Nuclease A inhibitor (NuiA) Superfamily:Nuclease A inhibitor (NuiA) Family:Nuclease A inhibitor (NuiA) 15 d2oqea1 8.5 22 Fold:Supersandwich Superfamily:Amine oxidase catalytic domain Family:Amine oxidase catalytic domain 16 d1zcca1 7.8 13 Fold:TIM beta/alpha-barrel Superfamily:PLC-like phosphodiesterases Family:Glycerophosphoryl diester phosphodiesterase 17 d1tz9a_ 7.7 20 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:UxuA-like 18 d1o4ya_ 7.7 28 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Glycosyl hydrolases family 16 19 c2dnfA_ 7.5 16 PDB header:protein binding Chain: A: PDB Molecule:doublecortin domain-containing protein 2; PDBTitle: solution structure of rsgi ruh-062, a dcx domain from human 20 c3elkA_ 7.3 17 PDB header:transcription regulator Chain: A: PDB Molecule:putative transcriptional regulator ta0346; PDBTitle: crystal structure of putative transcriptional regulator ta0346 from2 thermoplasma acidophilum 21 c2y69S_ not modelled 6.7 30 PDB header:electron transport Chain: S: PDB Molecule:cytochrome c oxidase subunit 5b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 22 c1sfeA_ not modelled 6.5 6 PDB header:dna-binding protein Chain: A: PDB Molecule:ada o6-methylguanine-dna methyltransferase; PDBTitle: ada o6-methylguanine-dna methyltransferase from escherichia coli 23 c2j5gL_ not modelled 6.4 14 PDB header:hydrolase Chain: L: PDB Molecule:alr4455 protein; PDBTitle: the native structure of a beta-diketone hydrolase from the2 cyanobacterium anabaena sp. pcc 7120 24 c3ilnB_ not modelled 6.0 11 PDB header:hydrolase Chain: B: PDB Molecule:laminarinase; PDBTitle: x-ray structure of the laminarinase from rhodothermus marinus 25 d1szoa_ not modelled 5.8 14 Fold:ClpP/crotonase Superfamily:ClpP/crotonase Family:Crotonase-like 26 c2da1A_ not modelled 5.4 29 PDB header:transcription Chain: A: PDB Molecule:alpha-fetoprotein enhancer binding protein; PDBTitle: solution structure of the first homeobox domain of at-2 binding transcription factor 1 (atbf1) 27 c2b26A_ not modelled 5.4 29 PDB header:chaperone/protein transport Chain: A: PDB Molecule:sis1 protein; PDBTitle: the crystal structure of the protein complex of yeast hsp402 sis1 and hsp70 ssa1 28 c2nu9E_ not modelled 5.3 24 PDB header:ligase Chain: E: PDB Molecule:succinyl-coa synthetase beta chain; PDBTitle: c123at mutant of e. coli succinyl-coa synthetase2 orthorhombic crystal form

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