Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	Q	K	P	L	I	K	Q	G	Y	S	L	A	E	E	I	A	N	S	V	S	H	G	I	G	L	V	F	G	I	V	G	L	V	L	L	L	V	Q	A	V	D	L	N	A	S	A	T	A	I	T	S	Y	S	L	Y	G	G	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																																?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	I	L	L	F	L	A	S	T	L	Y	H	A	I	P	H	Q	R	A	K	M	W	L	K	K	F	D	H	C	A	I	Y	L	L	I	A	G	T	Y	T	P	F	L	L	V	G	L	D	S	P	L	A	R	G	L	M	I	V	I	W
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	L	A	L	L	G	I	L	F	K	L	T	I	A	H	R	F	K	I	L	S	L	V	T	Y	L	A	M	G	W	L	S	L	V	V	I	Y	E	M	A	V	K	L	A	A	G	S	V	T	L	L	A	V	G	G	V	V	Y	S	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.
Sequence		G	V	I	F	Y	V	C	K	R	I	P	Y	N	H	A	I	W	H	G	F	V	L	G	G	S	V	C	H	F	L	A	I	Y	L	Y	I	G	Q	A
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 1xl3 chain C domain 1 Region: 188 - 200 Aligned: 13 Modelled: 13 Confidence: 25.7% Identity: 31% Fold: Type III secretion system domain Superfamily: Type III secretion system domain Family: TyeA-like Phyre2 PDB 2e74 chain G domain 1 Region: 172 - 186 Aligned: 15 Modelled: 15 Confidence: 20.3% Identity: 40% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1vf5 chain G Region: 172 - 186 Aligned: 15 Modelled: 15 Confidence: 20.0% Identity: 40% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1vf5 chain G Region: 172 - 186 Aligned: 15 Modelled: 15 Confidence: 20.0% Identity: 40% PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2jv7 chain A Region: 4 - 24 Aligned: 21 Modelled: 21 Confidence: 19.9% Identity: 10% PDB header:metal binding protein Chain: A: PDB Molecule:calcium-binding protein; PDBTitle: nmr solution structure of histoplasma capsulatum cbp2 homodimer Phyre2 PDB 1srb chain A Region: 1 - 7 Aligned: 7 Modelled: 7 Confidence: 12.1% Identity: 29% PDB header:toxin Chain: A: PDB Molecule:sarafotoxins precursor; PDBTitle: conformational studies on srtb, a non-selective endothelin2 receptor agonist, and on irl 1620, an etb receptor3 specific agonist Phyre2 PDB 1ik7 chain A Region: 188 - 214 Aligned: 27 Modelled: 27 Confidence: 12.0% Identity: 26% Fold: DEATH domain Superfamily: DEATH domain Family: DEATH domain, DD Phyre2 PDB 2khs chain B Region: 3 - 22 Aligned: 20 Modelled: 20 Confidence: 9.4% Identity: 25% PDB header:hydrolase Chain: B: PDB Molecule:nuclease; PDBTitle: solution structure of snase121:snase(111-143) complex Phyre2 PDB 1rkc chain B Region: 2 - 10 Aligned: 9 Modelled: 9 Confidence: 9.3% Identity: 33% PDB header:cell adhesion, structural protein Chain: B: PDB Molecule:talin; PDBTitle: human vinculin head (1-258) in complex with talin's2 vinculin binding site 3 (residues 1944-1969) Phyre2 PDB 2kkt chain A Region: 2 - 10 Aligned: 9 Modelled: 9 Confidence: 8.9% Identity: 11% PDB header:transcription Chain: A: PDB Molecule:ataxin-7-like protein 3; PDBTitle: solution structure of the sca7 domain of human ataxin-7-l3 protein Phyre2 PDB 1mul chain A Region: 1 - 33 Aligned: 33 Modelled: 33 Confidence: 6.8% Identity: 15% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 2xse chain A Region: 1 - 48 Aligned: 48 Modelled: 48 Confidence: 6.7% Identity: 8% PDB header:oxidoreductase Chain: A: PDB Molecule:thymine dioxygenase jbp1; PDBTitle: the structural basis for recognition of j-base containing2 dna by a novel dna-binding domain in jbp1 Phyre2 PDB 1owf chain B Region: 1 - 10 Aligned: 10 Modelled: 10 Confidence: 6.6% Identity: 30% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 2o97 chain B domain 1 Region: 1 - 10 Aligned: 10 Modelled: 10 Confidence: 6.6% Identity: 30% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 1p71 chain A Region: 1 - 10 Aligned: 10 Modelled: 10 Confidence: 6.5% Identity: 20% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 3kb4 chain D Region: 185 - 201 Aligned: 17 Modelled: 17 Confidence: 6.4% Identity: 24% PDB header:structural genomics, unknown function Chain: D: PDB Molecule:alr8543 protein; PDBTitle: crystal structure of the alr8543 protein in complex with2 geranylgeranyl monophosphate and magnesium ion from nostoc sp. pcc3 7120, northeast structural genomics consortium target nsr141 Phyre2 PDB 2ldf chain A Region: 1 - 7 Aligned: 7 Modelled: 7 Confidence: 6.1% Identity: 14% PDB header:toxin Chain: A: PDB Molecule:sarafotoxin-m; PDBTitle: solution structure of the long sarafotoxin srtx-m Phyre2 PDB 2koe chain A Region: 56 - 68 Aligned: 13 Modelled: 13 Confidence: 5.9% Identity: 23% PDB header:membrane protein, signaling protein Chain: A: PDB Molecule:human cannabinoid receptor 1 - helix 7/8 peptide; PDBTitle: human cannabinoid receptor 1 - helix 7/8 peptide Phyre2 PDB 3msq chain C Region: 185 - 201 Aligned: 17 Modelled: 17 Confidence: 5.7% Identity: 24% PDB header:biosynthetic protein Chain: C: PDB Molecule:putative ubiquinone biosynthesis protein; PDBTitle: crystal structure of a putative ubiquinone biosynthesis protein2 (npun02000094) from nostoc punctiforme pcc 73102 at 2.85 a resolution Phyre2 PDB 3s90 chain D Region: 3 - 19 Aligned: 17 Modelled: 17 Confidence: 5.3% Identity: 18% PDB header:cell adhesion Chain: D: PDB Molecule:talin-1; PDBTitle: human vinculin head domain vh1 (residues 1-252) in complex with murine2 talin (vbs33; residues 1512-1546) Phyre2 1 d1xl3c1 2 d2e74g1 3 d1vf5g_ 4 c1vf5G_ 5 c2jv7A_ 6 c1srbA_ 7 d1ik7a_ 8 c2khsB_ 9 c1rkcB_ 10 c2kktA_ 11 d1mula_ 12 c2xseA_ 13 d1owfb_ 14 d2o97b1 15 d1p71a_ 16 c3kb4D_ 17 c2ldfA_ 18 c2koeA_ 19 c3msqC_ 20 c3s90D_ 21 22 23 24

Detailed template information

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

1 d1xl3c1 25.7 31 Fold:Type III secretion system domain Superfamily:Type III secretion system domain Family:TyeA-like 2 d2e74g1 20.3 40 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 3 d1vf5g_ 20.0 40 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 4 c1vf5G_ 20.0 40 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 5 c2jv7A_ 19.9 10 PDB header:metal binding protein Chain: A: PDB Molecule:calcium-binding protein; PDBTitle: nmr solution structure of histoplasma capsulatum cbp2 homodimer 6 c1srbA_ 12.1 29 PDB header:toxin Chain: A: PDB Molecule:sarafotoxins precursor; PDBTitle: conformational studies on srtb, a non-selective endothelin2 receptor agonist, and on irl 1620, an etb receptor3 specific agonist 7 d1ik7a_ 12.0 26 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 8 c2khsB_ 9.4 25 PDB header:hydrolase Chain: B: PDB Molecule:nuclease; PDBTitle: solution structure of snase121:snase(111-143) complex 9 c1rkcB_ 9.3 33 PDB header:cell adhesion, structural protein Chain: B: PDB Molecule:talin; PDBTitle: human vinculin head (1-258) in complex with talin's2 vinculin binding site 3 (residues 1944-1969) 10 c2kktA_ 8.9 11 PDB header:transcription Chain: A: PDB Molecule:ataxin-7-like protein 3; PDBTitle: solution structure of the sca7 domain of human ataxin-7-l3 protein 11 d1mula_ 6.8 15 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 12 c2xseA_ 6.7 8 PDB header:oxidoreductase Chain: A: PDB Molecule:thymine dioxygenase jbp1; PDBTitle: the structural basis for recognition of j-base containing2 dna by a novel dna-binding domain in jbp1 13 d1owfb_ 6.6 30 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 14 d2o97b1 6.6 30 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 15 d1p71a_ 6.5 20 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 16 c3kb4D_ 6.4 24 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:alr8543 protein; PDBTitle: crystal structure of the alr8543 protein in complex with2 geranylgeranyl monophosphate and magnesium ion from nostoc sp. pcc3 7120, northeast structural genomics consortium target nsr141 17 c2ldfA_ 6.1 14 PDB header:toxin Chain: A: PDB Molecule:sarafotoxin-m; PDBTitle: solution structure of the long sarafotoxin srtx-m 18 c2koeA_ 5.9 23 PDB header:membrane protein, signaling protein Chain: A: PDB Molecule:human cannabinoid receptor 1 - helix 7/8 peptide; PDBTitle: human cannabinoid receptor 1 - helix 7/8 peptide 19 c3msqC_ 5.7 24 PDB header:biosynthetic protein Chain: C: PDB Molecule:putative ubiquinone biosynthesis protein; PDBTitle: crystal structure of a putative ubiquinone biosynthesis protein2 (npun02000094) from nostoc punctiforme pcc 73102 at 2.85 a resolution 20 c3s90D_ 5.3 18 PDB header:cell adhesion Chain: D: PDB Molecule:talin-1; PDBTitle: human vinculin head domain vh1 (residues 1-252) in complex with murine2 talin (vbs33; residues 1512-1546) 21 d1exea_ not modelled 5.2 27 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 22 c2wy3B_ not modelled 5.1 12 PDB header:immune system/viral protein Chain: B: PDB Molecule:uncharacterized protein ul16; PDBTitle: structure of the hcmv ul16-micb complex elucidates select2 binding of a viral immunoevasin to diverse nkg2d ligands 23 c2kkrA_ not modelled 5.1 22 PDB header:transcription, protein binding Chain: A: PDB Molecule:ataxin-7; PDBTitle: solution structure of sca7 zinc finger domain from human ataxin-72 protein 24 c1unvA_ not modelled 5.1 17 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles

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