Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	A	T	K	D	P	E	F	E	N	R	I	N	T	N	K	S	P	R	N	A	A	T	C	R	G	R	Y	E	K	Q	A	K	G	E	F	L	M	S	D	M	L	A	V	E	Q	E	T	N	N	D	V	R	Q	F	L	N	K	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?			?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?											?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	E	L	R	N	K	A	P	K	N	E	E	T	K	H	E	E	H	T	P	D	N	H	E	E	T	D	H	H	E	A	K	Q	Q	E	Q	A	W	R	G	N	L	R	Y	L	D	T	L	N	R	L	D	E	V	L	P	R	K	L	Y
Secondary structure
SS confidence
Disorder					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?										?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		E	R	W	E	K	E	H	T	V	N	D	E	A	V	L	R	A	L	C	Y	F	A	G	T	G	K	N	S	Q	L	G	W	C	R	V	G	R	G	T	I	D	K	R	A	R	L	S	K	N	T	V	K	K	C	L	D	R	L	V	N
Secondary structure
SS confidence
Disorder						?		?	?	?																															?	?	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.
Sequence		H	F	K	L	V	E	R	T	E	G	Y	I	P	G	S	A	E	R	E	C	N	E	Y	Q	L	L	F	K	P	Y	N	M	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 2v79 chain B Region: 114 - 181 Aligned: 62 Modelled: 68 Confidence: 76.1% Identity: 11% PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis Phyre2 PDB 3h8d chain E Region: 52 - 62 Aligned: 11 Modelled: 11 Confidence: 34.8% Identity: 73% PDB header:motor protein/signaling protein Chain: E: PDB Molecule:disabled homolog 2; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide Phyre2 PDB 1vje chain A Region: 170 - 203 Aligned: 34 Modelled: 34 Confidence: 33.6% Identity: 24% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 2vn2 chain B Region: 114 - 180 Aligned: 61 Modelled: 67 Confidence: 32.4% Identity: 20% PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 Phyre2 PDB 2r7c chain A domain 2 Region: 7 - 53 Aligned: 47 Modelled: 47 Confidence: 23.6% Identity: 28% Fold: Rotavirus NSP2 fragment, N-terminal domain Superfamily: Rotavirus NSP2 fragment, N-terminal domain Family: Rotavirus NSP2 fragment, N-terminal domain Phyre2 PDB 2k5c chain A Region: 34 - 85 Aligned: 52 Modelled: 52 Confidence: 14.4% Identity: 31% PDB header:metal binding protein Chain: A: PDB Molecule:uncharacterized protein pf0385; PDBTitle: nmr structure for pf0385 Phyre2 PDB 2r7c chain A Region: 7 - 53 Aligned: 47 Modelled: 47 Confidence: 10.2% Identity: 28% PDB header:rna binding protein Chain: A: PDB Molecule:non-structural rna-binding protein 35; PDBTitle: crystallographic and biochemical analysis of rotavirus nsp22 with nucleotides reveals an ndp kinase like activity Phyre2 PDB 1j6x chain A Region: 170 - 206 Aligned: 36 Modelled: 37 Confidence: 8.8% Identity: 19% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 3zqu chain A Region: 103 - 129 Aligned: 22 Modelled: 27 Confidence: 8.7% Identity: 41% PDB header:lyase Chain: A: PDB Molecule:probable aromatic acid decarboxylase; PDBTitle: structure of a probable aromatic acid decarboxylase Phyre2 PDB 2fmm chain E domain 1 Region: 129 - 171 Aligned: 41 Modelled: 43 Confidence: 7.9% Identity: 32% Fold: ENT-like Superfamily: ENT-like Family: Emsy N terminal (ENT) domain-like Phyre2 PDB 3iyd chain E Region: 170 - 185 Aligned: 16 Modelled: 16 Confidence: 7.4% Identity: 38% PDB header:transcription/dna Chain: E: PDB Molecule:dna-directed rna polymerase subunit omega; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex Phyre2 PDB 2fmm chain E Region: 129 - 171 Aligned: 41 Modelled: 43 Confidence: 7.1% Identity: 32% PDB header:transcription Chain: E: PDB Molecule:protein emsy; PDBTitle: crystal structure of emsy-hp1 complex Phyre2 PDB 1p6r chain A Region: 166 - 204 Aligned: 39 Modelled: 39 Confidence: 6.9% Identity: 31% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Penicillinase repressor Phyre2 PDB 2j9w chain B Region: 39 - 60 Aligned: 22 Modelled: 22 Confidence: 6.8% Identity: 32% PDB header:protein transport Chain: B: PDB Molecule:vps28-prov protein; PDBTitle: structural insight into the escrt-i-ii link and its role in2 mvb trafficking Phyre2 PDB 2j9u chain A domain 1 Region: 39 - 60 Aligned: 22 Modelled: 22 Confidence: 6.8% Identity: 14% Fold: Four-helical up-and-down bundle Superfamily: VPS28 C-terminal domain-like Family: VPS28 C-terminal domain-like Phyre2 PDB 3dom chain C Region: 42 - 59 Aligned: 18 Modelled: 18 Confidence: 5.6% Identity: 22% PDB header:transcription Chain: C: PDB Molecule:rna polymerase ii transcription factor b subunit 2; PDBTitle: crystal structure of the complex between tfb5 and the c-terminal2 domain of tfb2 Phyre2 PDB 1j6w chain A Region: 170 - 203 Aligned: 34 Modelled: 34 Confidence: 5.5% Identity: 18% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 9wga chain A domain 2 Region: 148 - 156 Aligned: 9 Modelled: 9 Confidence: 5.5% Identity: 56% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Plant lectins/antimicrobial peptides Family: Hevein-like agglutinin (lectin) domain Phyre2 PDB 2cwg chain A domain 2 Region: 148 - 156 Aligned: 9 Modelled: 9 Confidence: 5.3% Identity: 56% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Plant lectins/antimicrobial peptides Family: Hevein-like agglutinin (lectin) domain Phyre2 PDB 2gu0 chain A Region: 7 - 16 Aligned: 10 Modelled: 10 Confidence: 5.0% Identity: 70% PDB header:viral protein Chain: A: PDB Molecule:nonstructural protein 2; PDBTitle: crystal structure of human rotavirus nsp2 (group c /2 bristol strain) Phyre2 1 c2v79B_ 2 c3h8dE_ 3 d1vjea_ 4 c2vn2B_ 5 d2r7ca2 6 c2k5cA_ 7 c2r7cA_ 8 d1j6xa_ 9 c3zquA_ 10 d2fmme1 11 c3iydE_ 12 c2fmmE_ 13 d1p6ra_ 14 c2j9wB_ 15 d2j9ua1 16 c3domC_ 17 d1j6wa_ 18 d9wgaa2 19 d2cwga2 20 c2gu0A_

Detailed template information

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

1 c2v79B_ 76.1 11 PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis 2 c3h8dE_ 34.8 73 PDB header:motor protein/signaling protein Chain: E: PDB Molecule:disabled homolog 2; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide 3 d1vjea_ 33.6 24 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 4 c2vn2B_ 32.4 20 PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 5 d2r7ca2 23.6 28 Fold:Rotavirus NSP2 fragment, N-terminal domain Superfamily:Rotavirus NSP2 fragment, N-terminal domain Family:Rotavirus NSP2 fragment, N-terminal domain 6 c2k5cA_ 14.4 31 PDB header:metal binding protein Chain: A: PDB Molecule:uncharacterized protein pf0385; PDBTitle: nmr structure for pf0385 7 c2r7cA_ 10.2 28 PDB header:rna binding protein Chain: A: PDB Molecule:non-structural rna-binding protein 35; PDBTitle: crystallographic and biochemical analysis of rotavirus nsp22 with nucleotides reveals an ndp kinase like activity 8 d1j6xa_ 8.8 19 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 9 c3zquA_ 8.7 41 PDB header:lyase Chain: A: PDB Molecule:probable aromatic acid decarboxylase; PDBTitle: structure of a probable aromatic acid decarboxylase 10 d2fmme1 7.9 32 Fold:ENT-like Superfamily:ENT-like Family:Emsy N terminal (ENT) domain-like 11 c3iydE_ 7.4 38 PDB header:transcription/dna Chain: E: PDB Molecule:dna-directed rna polymerase subunit omega; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex 12 c2fmmE_ 7.1 32 PDB header:transcription Chain: E: PDB Molecule:protein emsy; PDBTitle: crystal structure of emsy-hp1 complex 13 d1p6ra_ 6.9 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Penicillinase repressor 14 c2j9wB_ 6.8 32 PDB header:protein transport Chain: B: PDB Molecule:vps28-prov protein; PDBTitle: structural insight into the escrt-i-ii link and its role in2 mvb trafficking 15 d2j9ua1 6.8 14 Fold:Four-helical up-and-down bundle Superfamily:VPS28 C-terminal domain-like Family:VPS28 C-terminal domain-like 16 c3domC_ 5.6 22 PDB header:transcription Chain: C: PDB Molecule:rna polymerase ii transcription factor b subunit 2; PDBTitle: crystal structure of the complex between tfb5 and the c-terminal2 domain of tfb2 17 d1j6wa_ 5.5 18 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 18 d9wgaa2 5.5 56 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Plant lectins/antimicrobial peptides Family:Hevein-like agglutinin (lectin) domain 19 d2cwga2 5.3 56 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Plant lectins/antimicrobial peptides Family:Hevein-like agglutinin (lectin) domain 20 c2gu0A_ 5.0 70 PDB header:viral protein Chain: A: PDB Molecule:nonstructural protein 2; PDBTitle: crystal structure of human rotavirus nsp2 (group c /2 bristol strain)

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