Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	V	T	N	D	D	Y	I	R	L	L	S	A	L	L	P	P	G	P	V	W	S	A	S	D	P	A	I	A	G	A	A	P	S	L	T	R	V	H	Q	R	A	D	A	L	M	R	E	L	D	P	R	T	T	T	E	L	I	N
Secondary structure
SS confidence
Disorder		?	?	?	?														?						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	W	E	R	L	C	G	L	P	D	E	C	I	P	A	G	T	Q	T	L	R	Q	R	Q	Q	R	L	D	A	K	V	N	L	A	G	G	I	N	E	D	F	Y	L	A	Q	L	A	A	L	G	R	P	D	A	T	I	T	R	Y	D
Secondary structure
SS confidence
Disorder													?	?	?	?	?	?	?														?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	S	T	F	T	C	S	S	A	C	T	D	A	V	N	A	P	E	W	R	Y	Y	W	Q	V	N	M	P	A	T	T	N	S	T	W	M	T	C	G	D	P	C	D	S	A	L	R	I	W	G	D	T	V	V	E	C	V	L	N	K
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.
Sequence		L	C	P	S	H	T	Y	V	I	F	K	Y	P	E
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 1mhm chain A Region: 130 - 190 Aligned: 61 Modelled: 61 Confidence: 34.8% Identity: 16% PDB header:lyase Chain: A: PDB Molecule:s-adenosylmethionine decarboxylase; PDBTitle: crystal structure of s-adenosylmethionine decarboxylase2 from potato Phyre2 PDB 3ibp chain A Region: 80 - 111 Aligned: 32 Modelled: 32 Confidence: 31.5% Identity: 16% PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: the crystal structure of the dimerization domain of escherichia coli2 structural maintenance of chromosomes protein mukb Phyre2 PDB 1msv chain B Region: 130 - 190 Aligned: 58 Modelled: 61 Confidence: 28.3% Identity: 12% PDB header:lyase Chain: B: PDB Molecule:s-adenosylmethionine decarboxylase proenzyme; PDBTitle: the s68a s-adenosylmethionine decarboxylase proenzyme2 processing mutant. Phyre2 PDB 3ep3 chain A Region: 130 - 190 Aligned: 58 Modelled: 61 Confidence: 23.2% Identity: 12% PDB header:lyase Chain: A: PDB Molecule:s-adenosylmethionine decarboxylase alpha chain; PDBTitle: human adometdc d174n mutant with no putrescine bound Phyre2 PDB 1jl0 chain A Region: 130 - 190 Aligned: 58 Modelled: 61 Confidence: 21.4% Identity: 12% Fold: S-adenosylmethionine decarboxylase Superfamily: S-adenosylmethionine decarboxylase Family: S-adenosylmethionine decarboxylase Phyre2 PDB 1lva chain A domain 3 Region: 81 - 111 Aligned: 31 Modelled: 31 Confidence: 11.2% Identity: 0% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: C-terminal fragment of elongation factor SelB Phyre2 PDB 1l1o chain C Region: 128 - 177 Aligned: 50 Modelled: 50 Confidence: 9.7% Identity: 16% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 3pcq chain M Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 8.1% Identity: 32% PDB header:photosynthesis Chain: M: PDB Molecule:photosystem i reaction center subunit xii; PDBTitle: femtosecond x-ray protein nanocrystallography Phyre2 PDB 1mj5 chain A Region: 171 - 185 Aligned: 15 Modelled: 15 Confidence: 7.5% Identity: 20% Fold: alpha/beta-Hydrolases Superfamily: alpha/beta-Hydrolases Family: Haloalkane dehalogenase Phyre2 PDB 2wmm chain A Region: 80 - 111 Aligned: 32 Modelled: 32 Confidence: 7.1% Identity: 13% PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: crystal structure of the hinge domain of mukb Phyre2 PDB 1wsu chain A Region: 76 - 110 Aligned: 34 Modelled: 35 Confidence: 5.8% Identity: 12% PDB header:translation/rna Chain: A: PDB Molecule:selenocysteine-specific elongation factor; PDBTitle: c-terminal domain of elongation factor selb complexed with2 secis rna Phyre2 PDB 2q0o chain A Region: 57 - 110 Aligned: 44 Modelled: 54 Confidence: 5.6% Identity: 20% PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing Phyre2 PDB 3mqz chain A Region: 55 - 142 Aligned: 72 Modelled: 88 Confidence: 5.2% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized conserved protein duf1054; PDBTitle: crystal structure of conserved protein duf1054 from pink subaerial2 biofilm microbial leptospirillum sp. group ii uba. Phyre2 1 c1mhmA_ 2 c3ibpA_ 3 c1msvB_ 4 c3ep3A_ 5 d1jl0a_ 6 d1lvaa3 7 d1l1oc_ 8 c3pcqM_ 9 d1mj5a_ 10 c2wmmA_ 11 c1wsuA_ 12 c2q0oA_ 13 c3mqzA_

Detailed template information

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

1 c1mhmA_ 34.8 16 PDB header:lyase Chain: A: PDB Molecule:s-adenosylmethionine decarboxylase; PDBTitle: crystal structure of s-adenosylmethionine decarboxylase2 from potato 2 c3ibpA_ 31.5 16 PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: the crystal structure of the dimerization domain of escherichia coli2 structural maintenance of chromosomes protein mukb 3 c1msvB_ 28.3 12 PDB header:lyase Chain: B: PDB Molecule:s-adenosylmethionine decarboxylase proenzyme; PDBTitle: the s68a s-adenosylmethionine decarboxylase proenzyme2 processing mutant. 4 c3ep3A_ 23.2 12 PDB header:lyase Chain: A: PDB Molecule:s-adenosylmethionine decarboxylase alpha chain; PDBTitle: human adometdc d174n mutant with no putrescine bound 5 d1jl0a_ 21.4 12 Fold:S-adenosylmethionine decarboxylase Superfamily:S-adenosylmethionine decarboxylase Family:S-adenosylmethionine decarboxylase 6 d1lvaa3 11.2 0 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal fragment of elongation factor SelB 7 d1l1oc_ 9.7 16 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 8 c3pcqM_ 8.1 32 PDB header:photosynthesis Chain: M: PDB Molecule:photosystem i reaction center subunit xii; PDBTitle: femtosecond x-ray protein nanocrystallography 9 d1mj5a_ 7.5 20 Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:Haloalkane dehalogenase 10 c2wmmA_ 7.1 13 PDB header:cell cycle Chain: A: PDB Molecule:chromosome partition protein mukb; PDBTitle: crystal structure of the hinge domain of mukb 11 c1wsuA_ 5.8 12 PDB header:translation/rna Chain: A: PDB Molecule:selenocysteine-specific elongation factor; PDBTitle: c-terminal domain of elongation factor selb complexed with2 secis rna 12 c2q0oA_ 5.6 20 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 13 c3mqzA_ 5.2 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized conserved protein duf1054; PDBTitle: crystal structure of conserved protein duf1054 from pink subaerial2 biofilm microbial leptospirillum sp. group ii uba.

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