Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	G	F	F	Q	R	L	F	G	K	D	N	K	P	A	I	A	R	G	P	L	G	L	H	L	N	S	G	F	T	L	D	T	L	A	F	R	L	L	E	D	E	L	L	I	A	L	P	G	E	E	F	T	V	A	A	V	S	H
Secondary structure
SS confidence
Disorder		?	?	?	?				?			?	?	?	?	?	?	?	?	?									?				?							?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	D	L	G	G	G	S	Q	I	F	R	Y	Y	T	S	G	D	E	F	L	Q	I	N	T	T	G	G	E	D	I	D	D	I	D	D	I	K	L	F	V	Y	E	E	S	Y	G	I	S	K	E	S	H	W	R	E	A	I	N	A	K
Secondary structure
SS confidence
Disorder																										?		?	?	?	?	?		?																							?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	M	G	A	M	T	L	N	W	Q	E	K	R	W	Q	R	F	F	N	S	E	E	P	G	N	I	E	P	V	Y	M	L	E	K	V	E	N	Q	N	H	A	K	W	E	V	H	N	F	T	M	G	Y	Q	R	Q	V	T	E	D	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?		?		?	?									?	?	?	?																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.
Sequence		Y	E	Y	L	L	L	N	G	E	E	S	F	N	D	L	G	E	P	E	W	L	F	S	R	A	L	G	V	D	I	P	L	T	S	L	H	I	I	G
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 1wmx chain A Region: 42 - 152 Aligned: 103 Modelled: 111 Confidence: 19.1% Identity: 13% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 30 carbohydrate binding module, CBM30 (PKD repeat) Phyre2 PDB 3alx chain B Region: 147 - 211 Aligned: 44 Modelled: 45 Confidence: 16.9% Identity: 16% PDB header:viral protein/membrane protein Chain: B: PDB Molecule:hemagglutinin, cdw150; PDBTitle: crystal structure of the measles virus hemagglutinin bound to its2 cellular receptor slam (mv-h(l482r)-slam(n102h/r108y) fusion) Phyre2 PDB 1jmx chain A domain 2 Region: 109 - 139 Aligned: 31 Modelled: 31 Confidence: 15.5% Identity: 16% Fold: Cytochrome c Superfamily: Cytochrome c Family: Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 Phyre2 PDB 2kxo chain A Region: 3 - 17 Aligned: 15 Modelled: 15 Confidence: 15.3% Identity: 33% PDB header:cell cycle Chain: A: PDB Molecule:cell division topological specificity factor; PDBTitle: solution nmr structure of the cell division regulator mine protein2 from neisseria gonorrhoeae Phyre2 PDB 1pby chain A domain 2 Region: 109 - 139 Aligned: 31 Modelled: 31 Confidence: 12.3% Identity: 19% Fold: Cytochrome c Superfamily: Cytochrome c Family: Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 Phyre2 PDB 1gla chain F Region: 3 - 83 Aligned: 80 Modelled: 81 Confidence: 9.9% Identity: 18% Fold: Barrel-sandwich hybrid Superfamily: Duplicated hybrid motif Family: Glucose permease-like Phyre2 PDB 2dhz chain A Region: 170 - 209 Aligned: 40 Modelled: 40 Confidence: 8.6% Identity: 20% PDB header:signaling protein Chain: A: PDB Molecule:rap guanine nucleotide exchange factor (gef)- PDBTitle: solution structure of the ra domain in the human link2 guanine nucleotide exchange factor ii (link-gefii) Phyre2 PDB 3pmg chain A domain 4 Region: 98 - 149 Aligned: 51 Modelled: 52 Confidence: 7.7% Identity: 10% Fold: TBP-like Superfamily: Phosphoglucomutase, C-terminal domain Family: Phosphoglucomutase, C-terminal domain Phyre2 PDB 1pby chain A Region: 109 - 148 Aligned: 40 Modelled: 40 Confidence: 6.3% Identity: 20% PDB header:oxidoreductase Chain: A: PDB Molecule:quinohemoprotein amine dehydrogenase 60 kda PDBTitle: structure of the phenylhydrazine adduct of the2 quinohemoprotein amine dehydrogenase from paracoccus3 denitrificans at 1.7 a resolution Phyre2 PDB 2bid chain A Region: 87 - 131 Aligned: 45 Modelled: 45 Confidence: 5.8% Identity: 9% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1jmx chain A Region: 109 - 139 Aligned: 31 Modelled: 31 Confidence: 5.5% Identity: 16% PDB header:oxidoreductase Chain: A: PDB Molecule:amine dehydrogenase; PDBTitle: crystal structure of a quinohemoprotein amine dehydrogenase2 from pseudomonas putida Phyre2 PDB 2ewc chain A domain 1 Region: 5 - 38 Aligned: 33 Modelled: 34 Confidence: 5.3% Identity: 21% Fold: Bacillus chorismate mutase-like Superfamily: YjgF-like Family: YjgF/L-PSP Phyre2 PDB 2jeu chain A Region: 131 - 167 Aligned: 37 Modelled: 37 Confidence: 5.2% Identity: 8% PDB header:transcription Chain: A: PDB Molecule:regulatory protein e2; PDBTitle: transcription activator structure reveals redox control of2 a replication initiation reaction Phyre2 1 d1wmxa_ 2 c3alxB_ 3 d1jmxa2 4 c2kxoA_ 5 d1pbya2 6 d1glaf_ 7 c2dhzA_ 8 d3pmga4 9 c1pbyA_ 10 d2bida_ 11 c1jmxA_ 12 d2ewca1 13 c2jeuA_

Detailed template information

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

1 d1wmxa_ 19.1 13 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 30 carbohydrate binding module, CBM30 (PKD repeat) 2 c3alxB_ 16.9 16 PDB header:viral protein/membrane protein Chain: B: PDB Molecule:hemagglutinin, cdw150; PDBTitle: crystal structure of the measles virus hemagglutinin bound to its2 cellular receptor slam (mv-h(l482r)-slam(n102h/r108y) fusion) 3 d1jmxa2 15.5 16 Fold:Cytochrome c Superfamily:Cytochrome c Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 4 c2kxoA_ 15.3 33 PDB header:cell cycle Chain: A: PDB Molecule:cell division topological specificity factor; PDBTitle: solution nmr structure of the cell division regulator mine protein2 from neisseria gonorrhoeae 5 d1pbya2 12.3 19 Fold:Cytochrome c Superfamily:Cytochrome c Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 6 d1glaf_ 9.9 18 Fold:Barrel-sandwich hybrid Superfamily:Duplicated hybrid motif Family:Glucose permease-like 7 c2dhzA_ 8.6 20 PDB header:signaling protein Chain: A: PDB Molecule:rap guanine nucleotide exchange factor (gef)- PDBTitle: solution structure of the ra domain in the human link2 guanine nucleotide exchange factor ii (link-gefii) 8 d3pmga4 7.7 10 Fold:TBP-like Superfamily:Phosphoglucomutase, C-terminal domain Family:Phosphoglucomutase, C-terminal domain 9 c1pbyA_ 6.3 20 PDB header:oxidoreductase Chain: A: PDB Molecule:quinohemoprotein amine dehydrogenase 60 kda PDBTitle: structure of the phenylhydrazine adduct of the2 quinohemoprotein amine dehydrogenase from paracoccus3 denitrificans at 1.7 a resolution 10 d2bida_ 5.8 9 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 11 c1jmxA_ 5.5 16 PDB header:oxidoreductase Chain: A: PDB Molecule:amine dehydrogenase; PDBTitle: crystal structure of a quinohemoprotein amine dehydrogenase2 from pseudomonas putida 12 d2ewca1 5.3 21 Fold:Bacillus chorismate mutase-like Superfamily:YjgF-like Family:YjgF/L-PSP 13 c2jeuA_ 5.2 8 PDB header:transcription Chain: A: PDB Molecule:regulatory protein e2; PDBTitle: transcription activator structure reveals redox control of2 a replication initiation reaction

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