Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	V	R	A	Q	R	I	Q	H	V	M	Q	D	T	I	I	N	F	Y	S	T	S	D	D	Y	G	D	F	S	N	F	A	A	W	P	I	K	V	D	G	K	T	W	P	T	S	E	H	Y	F	Q	A	Q	K	F	L	D	E	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	R	E	E	I	R	R	V	S	S	P	M	V	A	A	R	M	G	R	D	R	S	K	P	L	R	K	N	W	E	S	V	K	E	Q	V	M	R	K	A	L	R	A	K	F	E	Q	H	A	E	L	R	A	L	L	L	A	T	A	P
Secondary structure
SS confidence
Disorder																											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160
Sequence		A	K	L	V	E	H	T	E	N	D	A	Y	W	G	D	G	G	H	G	K	G	K	N	R	L	G	Y	L	L	M	E	L	R	E	Q	L	A	I	E	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 2b3w chain A domain 1 Region: 1 - 160 Aligned: 160 Modelled: 160 Confidence: 100.0% Identity: 100% Fold: YbiA-like Superfamily: YbiA-like Family: YbiA-like Phyre2 PDB 2k0m chain A Region: 36 - 84 Aligned: 48 Modelled: 49 Confidence: 45.3% Identity: 17% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of the uncharacterized protein from2 rhodospirillum rubrum gene locus rru_a0810. northeast3 structural genomics target rrr43 Phyre2 PDB 1w7c chain A domain 3 Region: 30 - 58 Aligned: 29 Modelled: 29 Confidence: 21.7% Identity: 17% Fold: Cystatin-like Superfamily: Amine oxidase N-terminal region Family: Amine oxidase N-terminal region Phyre2 PDB 2ff4 chain A domain 1 Region: 110 - 158 Aligned: 49 Modelled: 49 Confidence: 17.1% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: PhoB-like Phyre2 PDB 2oar chain A Region: 147 - 159 Aligned: 13 Modelled: 13 Confidence: 11.7% Identity: 46% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 1uur chain A domain 2 Region: 119 - 153 Aligned: 26 Modelled: 35 Confidence: 10.7% Identity: 19% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: p53-like transcription factors Family: STAT DNA-binding domain Phyre2 PDB 1avo chain D Region: 44 - 93 Aligned: 48 Modelled: 50 Confidence: 10.1% Identity: 19% PDB header:proteasome activator Chain: D: PDB Molecule:11s regulator; PDBTitle: proteasome activator reg(alpha) Phyre2 PDB 1gxq chain A Region: 110 - 158 Aligned: 48 Modelled: 49 Confidence: 8.9% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: PhoB-like Phyre2 PDB 2k4j chain A Region: 110 - 158 Aligned: 48 Modelled: 49 Confidence: 8.5% Identity: 10% PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: arsr dna binding domain Phyre2 PDB 1opc chain A Region: 110 - 156 Aligned: 46 Modelled: 47 Confidence: 7.5% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: PhoB-like Phyre2 PDB 1i3j chain A Region: 31 - 71 Aligned: 41 Modelled: 41 Confidence: 7.4% Identity: 10% Fold: DNA-binding domain of intron-encoded endonucleases Superfamily: DNA-binding domain of intron-encoded endonucleases Family: DNA-binding domain of intron-encoded endonucleases Phyre2 PDB 1kgs chain A domain 1 Region: 110 - 158 Aligned: 43 Modelled: 49 Confidence: 7.2% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: PhoB-like Phyre2 PDB 1mjd chain A Region: 6 - 53 Aligned: 42 Modelled: 48 Confidence: 6.4% Identity: 12% Fold: beta-Grasp (ubiquitin-like) Superfamily: Doublecortin (DC) Family: Doublecortin (DC) Phyre2 PDB 1mhy chain G Region: 59 - 153 Aligned: 95 Modelled: 95 Confidence: 6.2% Identity: 21% Fold: Open three-helical up-and-down bundle Superfamily: Methane monooxygenase hydrolase, gamma subunit Family: Methane monooxygenase hydrolase, gamma subunit Phyre2 PDB 2l2l chain A Region: 147 - 160 Aligned: 14 Modelled: 14 Confidence: 6.1% Identity: 29% PDB header:transferase Chain: A: PDB Molecule:transcriptional repressor p66-alpha; PDBTitle: solution structure of the coiled-coil complex between mbd2 and2 p66alpha Phyre2 PDB 1mjt chain A Region: 37 - 108 Aligned: 71 Modelled: 72 Confidence: 5.8% Identity: 15% Fold: Nitric oxide (NO) synthase oxygenase domain Superfamily: Nitric oxide (NO) synthase oxygenase domain Family: Nitric oxide (NO) synthase oxygenase domain Phyre2 PDB 1om4 chain A Region: 37 - 108 Aligned: 71 Modelled: 72 Confidence: 5.3% Identity: 15% Fold: Nitric oxide (NO) synthase oxygenase domain Superfamily: Nitric oxide (NO) synthase oxygenase domain Family: Nitric oxide (NO) synthase oxygenase domain Phyre2 1 d2b3wa1 2 c2k0mA_ 3 d1w7ca3 4 d2ff4a1 5 c2oarA_ 6 d1uura2 7 c1avoD_ 8 d1gxqa_ 9 c2k4jA_ 10 d1opca_ 11 d1i3ja_ 12 d1kgsa1 13 d1mjda_ 14 d1mhyg_ 15 c2l2lA_ 16 d1mjta_ 17 d1om4a_

Detailed template information

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

1 d2b3wa1 100.0 100 Fold:YbiA-like Superfamily:YbiA-like Family:YbiA-like 2 c2k0mA_ 45.3 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of the uncharacterized protein from2 rhodospirillum rubrum gene locus rru_a0810. northeast3 structural genomics target rrr43 3 d1w7ca3 21.7 17 Fold:Cystatin-like Superfamily:Amine oxidase N-terminal region Family:Amine oxidase N-terminal region 4 d2ff4a1 17.1 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like 5 c2oarA_ 11.7 46 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 6 d1uura2 10.7 19 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:p53-like transcription factors Family:STAT DNA-binding domain 7 c1avoD_ 10.1 19 PDB header:proteasome activator Chain: D: PDB Molecule:11s regulator; PDBTitle: proteasome activator reg(alpha) 8 d1gxqa_ 8.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like 9 c2k4jA_ 8.5 10 PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: arsr dna binding domain 10 d1opca_ 7.5 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like 11 d1i3ja_ 7.4 10 Fold:DNA-binding domain of intron-encoded endonucleases Superfamily:DNA-binding domain of intron-encoded endonucleases Family:DNA-binding domain of intron-encoded endonucleases 12 d1kgsa1 7.2 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:PhoB-like 13 d1mjda_ 6.4 12 Fold:beta-Grasp (ubiquitin-like) Superfamily:Doublecortin (DC) Family:Doublecortin (DC) 14 d1mhyg_ 6.2 21 Fold:Open three-helical up-and-down bundle Superfamily:Methane monooxygenase hydrolase, gamma subunit Family:Methane monooxygenase hydrolase, gamma subunit 15 c2l2lA_ 6.1 29 PDB header:transferase Chain: A: PDB Molecule:transcriptional repressor p66-alpha; PDBTitle: solution structure of the coiled-coil complex between mbd2 and2 p66alpha 16 d1mjta_ 5.8 15 Fold:Nitric oxide (NO) synthase oxygenase domain Superfamily:Nitric oxide (NO) synthase oxygenase domain Family:Nitric oxide (NO) synthase oxygenase domain 17 d1om4a_ 5.3 15 Fold:Nitric oxide (NO) synthase oxygenase domain Superfamily:Nitric oxide (NO) synthase oxygenase domain Family:Nitric oxide (NO) synthase oxygenase 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