Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	Y	K	L	L	P	C	L	L	A	I	F	L	T	G	C	D	R	T	E	V	T	L	S	F	T	P	E	M	A	S	F	S	N	E	F	D	F	D	P	L	R	G	P	V	K	D	F	T	Q	T	L	M	D	E	Q	G	E	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?												?	?		?	?	?	?					?																											?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	K	R	V	S	G	T	L	S	E	E	G	C	F	D	S	L	E	L	L	D	L	E	N	N	T	V	V	A	L	V	L	D	A	N	Y	Y	R	D	A	E	T	L	E	K	R	V	R	L	Q	G	K	C	Q	L	A	E	L	P	S
Secondary structure
SS confidence
Disorder																				?	?		?			?											?	?	?	?	?	?																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	G	V	S	W	E	T	D	D	N	G	F	V	I	K	A	S	S	K	Q	M	Q	M	E	Y	R	Y	D	D	Q	G	Y	P	L	G	K	T	T	K	S	N	D	K	T	L	S	V	S	A	T	P	S	T	D	P	I	K	K	L	D
Secondary structure
SS confidence
Disorder																		?	?			?																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.
Sequence		Y	T	A	V	T	L	L	N	N	Q	R	V	G	N	V	K	Q	S	C	E	Y	D	S	H	A	N	P	V	D	C	Q	L	I	I	V	D	E	G	V	K	P	A	V	E	R	V	Y	T	I	K	N	T	I	D	Y	Y
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 3n7x chain A Region: 41 - 81 Aligned: 41 Modelled: 41 Confidence: 52.5% Identity: 27% PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: crystal structure of penaeus stylirostris densovirus capsid Phyre2 PDB 1q5y chain A Region: 27 - 85 Aligned: 58 Modelled: 59 Confidence: 45.8% Identity: 12% Fold: Ferredoxin-like Superfamily: ACT-like Family: Nickel responsive regulator NikR, C-terminal domain Phyre2 PDB 2y3y chain C Region: 28 - 85 Aligned: 57 Modelled: 58 Confidence: 43.2% Identity: 12% PDB header:transcription Chain: C: PDB Molecule:putative nickel-responsive regulator; PDBTitle: holo-ni(ii) hpnikr is a symmetric tetramer containing four2 canonic square-planar ni(ii) ions at physiological ph Phyre2 PDB 2bj7 chain A domain 2 Region: 29 - 85 Aligned: 56 Modelled: 57 Confidence: 34.5% Identity: 9% Fold: Ferredoxin-like Superfamily: ACT-like Family: Nickel responsive regulator NikR, C-terminal domain Phyre2 PDB 1e8o chain A Region: 205 - 233 Aligned: 29 Modelled: 29 Confidence: 28.1% Identity: 10% Fold: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Phyre2 PDB 1914 chain A domain 1 Region: 206 - 233 Aligned: 28 Modelled: 28 Confidence: 22.7% Identity: 11% Fold: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Phyre2 PDB 2ca9 chain B Region: 28 - 85 Aligned: 57 Modelled: 58 Confidence: 21.5% Identity: 12% PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation Phyre2 PDB 2bj3 chain D Region: 28 - 77 Aligned: 47 Modelled: 50 Confidence: 20.9% Identity: 11% PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo Phyre2 PDB 2b5i chain B domain 1 Region: 198 - 223 Aligned: 26 Modelled: 26 Confidence: 20.8% Identity: 27% Fold: Immunoglobulin-like beta-sandwich Superfamily: Fibronectin type III Family: Fibronectin type III Phyre2 PDB 3seb chain A domain 1 Region: 26 - 51 Aligned: 26 Modelled: 26 Confidence: 20.1% Identity: 27% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Superantigen toxins, N-terminal domain Phyre2 PDB 3l4q chain A Region: 31 - 38 Aligned: 8 Modelled: 8 Confidence: 14.0% Identity: 63% PDB header:viral protein/protein binding Chain: A: PDB Molecule:non-structural protein 1; PDBTitle: structural insights into phosphoinositide 3-kinase2 activation by the influenza a virus ns1 protein Phyre2 PDB 3d6r chain A Region: 31 - 38 Aligned: 8 Modelled: 8 Confidence: 13.7% Identity: 63% PDB header:viral protein Chain: A: PDB Molecule:non-structural protein 1; PDBTitle: structure of an avian influenza a virus ns1 protein2 effector domain Phyre2 PDB 2gx9 chain A domain 1 Region: 31 - 38 Aligned: 8 Modelled: 8 Confidence: 13.6% Identity: 63% Fold: Ns1 effector domain-like Superfamily: Ns1 effector domain-like Family: Ns1 effector domain-like Phyre2 PDB 1c5c chain L domain 2 Region: 23 - 71 Aligned: 49 Modelled: 49 Confidence: 12.7% Identity: 16% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: C1 set domains (antibody constant domain-like) Phyre2 PDB 3f5t chain A Region: 31 - 38 Aligned: 8 Modelled: 8 Confidence: 11.3% Identity: 63% PDB header:viral protein Chain: A: PDB Molecule:nonstructural protein 1; PDBTitle: x-ray structure of h5n1 ns1 Phyre2 PDB 1914 chain A Region: 206 - 233 Aligned: 28 Modelled: 28 Confidence: 10.6% Identity: 11% PDB header:alu domain Chain: A: PDB Molecule:signal recognition particle 9/14 fusion protein; PDBTitle: signal recognition particle alu rna binding heterodimer, srp9/14 Phyre2 PDB 1bxt chain A domain 1 Region: 25 - 44 Aligned: 20 Modelled: 20 Confidence: 10.4% Identity: 25% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Superantigen toxins, N-terminal domain Phyre2 PDB 1hyr chain C domain 1 Region: 26 - 71 Aligned: 46 Modelled: 46 Confidence: 10.0% Identity: 20% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: C1 set domains (antibody constant domain-like) Phyre2 PDB 1je6 chain A domain 1 Region: 26 - 71 Aligned: 46 Modelled: 46 Confidence: 8.5% Identity: 17% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: C1 set domains (antibody constant domain-like) Phyre2 PDB 2e12 chain B Region: 46 - 70 Aligned: 25 Modelled: 25 Confidence: 8.2% Identity: 24% PDB header:translation Chain: B: PDB Molecule:hypothetical protein xcc3642; PDBTitle: the crystal structure of xc5848 from xanthomonas campestris2 adopting a novel variant of sm-like motif Phyre2 1 c3n7xA_ 2 d1q5ya_ 3 c2y3yC_ 4 d2bj7a2 5 d1e8oa_ 6 d1914a1 7 c2ca9B_ 8 c2bj3D_ 9 d2b5ib1 10 d3seba1 11 c3l4qA_ 12 c3d6rA_ 13 d2gx9a1 14 d1c5cl2 15 c3f5tA_ 16 c1914A_ 17 d1bxta1 18 d1hyrc1 19 d1je6a1 20 c2e12B_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 c3n7xA_ 52.5 27 PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: crystal structure of penaeus stylirostris densovirus capsid 2 d1q5ya_ 45.8 12 Fold:Ferredoxin-like Superfamily:ACT-like Family:Nickel responsive regulator NikR, C-terminal domain 3 c2y3yC_ 43.2 12 PDB header:transcription Chain: C: PDB Molecule:putative nickel-responsive regulator; PDBTitle: holo-ni(ii) hpnikr is a symmetric tetramer containing four2 canonic square-planar ni(ii) ions at physiological ph 4 d2bj7a2 34.5 9 Fold:Ferredoxin-like Superfamily:ACT-like Family:Nickel responsive regulator NikR, C-terminal domain 5 d1e8oa_ 28.1 10 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 6 d1914a1 22.7 11 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 7 c2ca9B_ 21.5 12 PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation 8 c2bj3D_ 20.9 11 PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo 9 d2b5ib1 20.8 27 Fold:Immunoglobulin-like beta-sandwich Superfamily:Fibronectin type III Family:Fibronectin type III 10 d3seba1 20.1 27 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Superantigen toxins, N-terminal domain 11 c3l4qA_ 14.0 63 PDB header:viral protein/protein binding Chain: A: PDB Molecule:non-structural protein 1; PDBTitle: structural insights into phosphoinositide 3-kinase2 activation by the influenza a virus ns1 protein 12 c3d6rA_ 13.7 63 PDB header:viral protein Chain: A: PDB Molecule:non-structural protein 1; PDBTitle: structure of an avian influenza a virus ns1 protein2 effector domain 13 d2gx9a1 13.6 63 Fold:Ns1 effector domain-like Superfamily:Ns1 effector domain-like Family:Ns1 effector domain-like 14 d1c5cl2 12.7 16 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C1 set domains (antibody constant domain-like) 15 c3f5tA_ 11.3 63 PDB header:viral protein Chain: A: PDB Molecule:nonstructural protein 1; PDBTitle: x-ray structure of h5n1 ns1 16 c1914A_ 10.6 11 PDB header:alu domain Chain: A: PDB Molecule:signal recognition particle 9/14 fusion protein; PDBTitle: signal recognition particle alu rna binding heterodimer, srp9/14 17 d1bxta1 10.4 25 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Superantigen toxins, N-terminal domain 18 d1hyrc1 10.0 20 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C1 set domains (antibody constant domain-like) 19 d1je6a1 8.5 17 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C1 set domains (antibody constant domain-like) 20 c2e12B_ 8.2 24 PDB header:translation Chain: B: PDB Molecule:hypothetical protein xcc3642; PDBTitle: the crystal structure of xc5848 from xanthomonas campestris2 adopting a novel variant of sm-like motif 21 c2ns6A_ not modelled 7.4 19 PDB header:hydrolase Chain: A: PDB Molecule:mobilization protein a; PDBTitle: crystal structure of the minimal relaxase domain of moba2 from plasmid r1162 22 c3d33B_ not modelled 7.2 17 PDB header:unknown function Chain: B: PDB Molecule:domain of unknown function with an immunoglobulin-like PDBTitle: crystal structure of a duf3244 family protein with an immunoglobulin-2 like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc3 8482 at 1.70 a resolution 23 c3mx7A_ not modelled 6.9 12 PDB header:apoptosis Chain: A: PDB Molecule:fas apoptotic inhibitory molecule 1; PDBTitle: crystal structure analysis of human faim-ntd 24 d1tzoa_ not modelled 6.7 16 Fold:Anthrax protective antigen Superfamily:Anthrax protective antigen Family:Anthrax protective antigen 25 d1irub_ not modelled 6.4 14 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Proteasome subunits 26 c1cqtJ_ not modelled 6.4 19 PDB header:gene regulation/dna Chain: J: PDB Molecule:pou domain, class 2, associating factor 1; PDBTitle: crystal structure of a ternary complex containing an oca-b2 peptide, the oct-1 pou domain, and an octamer element 27 c2p64B_ not modelled 6.1 16 PDB header:ligase Chain: B: PDB Molecule:f-box/wd repeat protein 1a; PDBTitle: d domain of b-trcp 28 d2q86b2 not modelled 6.1 13 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C1 set domains (antibody constant domain-like) 29 c3sqgF_ not modelled 5.6 28 PDB header:transferase Chain: F: PDB Molecule:methyl-coenzyme m reductase, gamma subunit; PDBTitle: crystal structure of a methyl-coenzyme m reductase purified from black2 sea mats 30 c3n1uA_ not modelled 5.2 20 PDB header:hydrolase Chain: A: PDB Molecule:hydrolase, had superfamily, subfamily iii a; PDBTitle: structure of putative had superfamily (subfamily iii a) hydrolase from2 legionella pneumophila

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