Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	Q	A	I	Q	F	P	D	R	E	E	W	D	E	N	K	K	C	V	C	F	P	A	L	V	N	G	M	Q	L	T	C	A	I	S	G	E	S	L	A	Y	R	F	T	G	D	T	P	E	Q	W	L	A	S	F	R	Q	H	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?					?															?										?								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.
Sequence		W	D	L	E	E	E	A	E	N	L	I	Q	E	Q	S	E	D	D	Q	G	W	V	W	L	P
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 2gpi chain A domain 1 Region: 1 - 84 Aligned: 84 Modelled: 83 Confidence: 100.0% Identity: 33% Fold: Shew3726-like Superfamily: Shew3726-like Family: Shew3726-like Phyre2 PDB 1pd3 chain A Region: 50 - 70 Aligned: 21 Modelled: 21 Confidence: 17.6% Identity: 38% Fold: ROP-like Superfamily: Nonstructural protein ns2, Nep, M1-binding domain Family: Nonstructural protein ns2, Nep, M1-binding domain Phyre2 PDB 3fhk chain F Region: 22 - 59 Aligned: 38 Modelled: 38 Confidence: 17.0% Identity: 18% PDB header:structural genomics, unknown function Chain: F: PDB Molecule:upf0403 protein yphp; PDBTitle: crystal structure of apc1446, b.subtilis yphp disulfide2 isomerase Phyre2 PDB 2rnm chain C Region: 2 - 10 Aligned: 9 Modelled: 9 Confidence: 16.4% Identity: 22% PDB header:protein fibril Chain: C: PDB Molecule:small s protein; PDBTitle: structure of the het-s(218-289) prion in its amyloid form2 obtained by solid-state nmr Phyre2 PDB 3c07 chain A domain 1 Region: 35 - 74 Aligned: 38 Modelled: 40 Confidence: 13.4% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Tetracyclin repressor-like, N-terminal domain Phyre2 PDB 3cta chain A domain 2 Region: 18 - 35 Aligned: 16 Modelled: 18 Confidence: 12.4% Identity: 25% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Riboflavin kinase-like Family: CTP-dependent riboflavin kinase-like Phyre2 PDB 1ou8 chain A Region: 16 - 49 Aligned: 34 Modelled: 34 Confidence: 11.9% Identity: 12% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 2dhy chain A Region: 36 - 72 Aligned: 37 Modelled: 37 Confidence: 10.9% Identity: 11% PDB header:immune system Chain: A: PDB Molecule:cue domain-containing protein 1; PDBTitle: solution structure of the cue domain in the human cue2 domain containing protein 1 (cuedc1) Phyre2 PDB 1zsz chain C domain 1 Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 10.1% Identity: 9% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 1yfn chain A domain 1 Region: 16 - 49 Aligned: 34 Modelled: 34 Confidence: 9.6% Identity: 12% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 1y67 chain A domain 2 Region: 37 - 84 Aligned: 33 Modelled: 48 Confidence: 9.0% Identity: 27% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1b06 chain A domain 2 Region: 37 - 84 Aligned: 33 Modelled: 48 Confidence: 8.8% Identity: 24% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1wb8 chain A domain 2 Region: 37 - 84 Aligned: 33 Modelled: 48 Confidence: 8.3% Identity: 24% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 2gyq chain A domain 1 Region: 37 - 70 Aligned: 34 Modelled: 34 Confidence: 8.0% Identity: 15% Fold: Ferritin-like Superfamily: Ferritin-like Family: YciF-like Phyre2 PDB 1s6l chain A domain 1 Region: 61 - 82 Aligned: 22 Modelled: 22 Confidence: 7.8% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MerB N-terminal domain-like Phyre2 PDB 1p7g chain L Region: 37 - 84 Aligned: 33 Modelled: 48 Confidence: 7.5% Identity: 27% PDB header:oxidoreductase Chain: L: PDB Molecule:superoxide dismutase; PDBTitle: crystal structure of superoxide dismutase from pyrobaculum2 aerophilum Phyre2 PDB 1ou9 chain A Region: 15 - 49 Aligned: 35 Modelled: 35 Confidence: 7.1% Identity: 11% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 1jr9 chain A domain 2 Region: 37 - 84 Aligned: 33 Modelled: 48 Confidence: 6.6% Identity: 21% Fold: Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily: Fe,Mn superoxide dismutase (SOD), C-terminal domain Family: Fe,Mn superoxide dismutase (SOD), C-terminal domain Phyre2 PDB 1q1l chain A Region: 37 - 63 Aligned: 27 Modelled: 27 Confidence: 6.0% Identity: 19% Fold: Chorismate synthase, AroC Superfamily: Chorismate synthase, AroC Family: Chorismate synthase, AroC Phyre2 PDB 1gv3 chain B Region: 37 - 84 Aligned: 33 Modelled: 48 Confidence: 6.0% Identity: 24% PDB header:manganese superoxide dismutase Chain: B: PDB Molecule:manganese superoxide dismutase; PDBTitle: the 2.0 angstrom resolution structure of the catalytic2 portion of a cyanobacterial membrane-bound manganese3 superoxide dismutase Phyre2 1 d2gpia1 2 d1pd3a_ 3 c3fhkF_ 4 c2rnmC_ 5 d3c07a1 6 d3ctaa2 7 d1ou8a_ 8 c2dhyA_ 9 d1zszc1 10 d1yfna1 11 d1y67a2 12 d1b06a2 13 d1wb8a2 14 d2gyqa1 15 d1s6la1 16 c1p7gL_ 17 d1ou9a_ 18 d1jr9a2 19 d1q1la_ 20 c1gv3B_ 21 22 23 24 25 26

Detailed template information

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

1 d2gpia1 100.0 33 Fold:Shew3726-like Superfamily:Shew3726-like Family:Shew3726-like 2 d1pd3a_ 17.6 38 Fold:ROP-like Superfamily:Nonstructural protein ns2, Nep, M1-binding domain Family:Nonstructural protein ns2, Nep, M1-binding domain 3 c3fhkF_ 17.0 18 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:upf0403 protein yphp; PDBTitle: crystal structure of apc1446, b.subtilis yphp disulfide2 isomerase 4 c2rnmC_ 16.4 22 PDB header:protein fibril Chain: C: PDB Molecule:small s protein; PDBTitle: structure of the het-s(218-289) prion in its amyloid form2 obtained by solid-state nmr 5 d3c07a1 13.4 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 6 d3ctaa2 12.4 25 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin kinase-like Family:CTP-dependent riboflavin kinase-like 7 d1ou8a_ 11.9 12 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 8 c2dhyA_ 10.9 11 PDB header:immune system Chain: A: PDB Molecule:cue domain-containing protein 1; PDBTitle: solution structure of the cue domain in the human cue2 domain containing protein 1 (cuedc1) 9 d1zszc1 10.1 9 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 10 d1yfna1 9.6 12 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 11 d1y67a2 9.0 27 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 12 d1b06a2 8.8 24 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 13 d1wb8a2 8.3 24 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 14 d2gyqa1 8.0 15 Fold:Ferritin-like Superfamily:Ferritin-like Family:YciF-like 15 d1s6la1 7.8 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 16 c1p7gL_ 7.5 27 PDB header:oxidoreductase Chain: L: PDB Molecule:superoxide dismutase; PDBTitle: crystal structure of superoxide dismutase from pyrobaculum2 aerophilum 17 d1ou9a_ 7.1 11 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 18 d1jr9a2 6.6 21 Fold:Fe,Mn superoxide dismutase (SOD), C-terminal domain Superfamily:Fe,Mn superoxide dismutase (SOD), C-terminal domain Family:Fe,Mn superoxide dismutase (SOD), C-terminal domain 19 d1q1la_ 6.0 19 Fold:Chorismate synthase, AroC Superfamily:Chorismate synthase, AroC Family:Chorismate synthase, AroC 20 c1gv3B_ 6.0 24 PDB header:manganese superoxide dismutase Chain: B: PDB Molecule:manganese superoxide dismutase; PDBTitle: the 2.0 angstrom resolution structure of the catalytic2 portion of a cyanobacterial membrane-bound manganese3 superoxide dismutase 21 c1ztbA_ not modelled 5.9 11 PDB header:ligase Chain: A: PDB Molecule:chorismate synthase; PDBTitle: crystal structure of chorismate synthase from mycobacterium2 tuberculosis 22 c2cw3A_ not modelled 5.8 21 PDB header:oxidoreductase Chain: A: PDB Molecule:iron superoxide dismutase; PDBTitle: x-ray structure of pmsod2, superoxide dismutase from2 perkinsus marinus 23 c1mngA_ not modelled 5.4 27 PDB header:oxidoreductase(superoxide acceptor) Chain: A: PDB Molecule:manganese superoxide dismutase; PDBTitle: structure-function in e. coli iron superoxide dismutase: comparisons2 with the manganese enzyme from t. thermophilus 24 d1wgla_ not modelled 5.3 14 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:CUE domain 25 d2g3qa1 not modelled 5.1 27 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 26 d2bgca1 not modelled 5.1 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like

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