Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	E	D	P	E	I	R	I	H	K	L	Q	P	C	T	Q	C	P	R	L	E	D	L	W	F	S	W	Y	F	R	Y	I	H	D	R	C	L	R	S	S	A	C	H	Q	D	I	H	G	A	S	L	Y	A	P	L	A	L	K	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	Y	E	V	Y	F	G	Y	D	C	T	L	R	K	Y	G	R	F	R	Q	K	L	P	V	K	T	D	F	R	K	N	G	A	R	R	R	P	V	T	G	R	S	P	R	T	G	E	E	A	Q	W	I	C	N	H	S	E	Q	V	R
Secondary structure
SS confidence
Disorder																									?	?		?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.
Sequence		P	E	A	F	I	I	G	S	V	C	C	F	S	G	M	I	Y	P	H	I	Q	R	P	D	P	V	N	R	S	M	N	D	Q
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 2nr1 chain A Region: 24 - 28 Aligned: 5 Modelled: 5 Confidence: 18.1% Identity: 80% PDB header:receptor Chain: A: PDB Molecule:nr1 m2; PDBTitle: transmembrane segment 2 of nmda receptor nr1, nmr, 102 structures Phyre2 PDB 1ffg chain B Region: 126 - 132 Aligned: 7 Modelled: 7 Confidence: 17.9% Identity: 57% Fold: Ferredoxin-like Superfamily: CheY-binding domain of CheA Family: CheY-binding domain of CheA Phyre2 PDB 1a0o chain H Region: 126 - 132 Aligned: 7 Modelled: 7 Confidence: 17.7% Identity: 57% PDB header:chemotaxis Chain: H: PDB Molecule:chea; PDBTitle: chey-binding domain of chea in complex with chey Phyre2 PDB 2ysr chain A Region: 78 - 138 Aligned: 55 Modelled: 61 Confidence: 13.4% Identity: 20% PDB header:signaling protein Chain: A: PDB Molecule:dep domain-containing protein 1; PDBTitle: solution structure of the dep domain from human dep domain-2 containing protein 1 Phyre2 PDB 2ld7 chain A Region: 71 - 90 Aligned: 19 Modelled: 20 Confidence: 11.6% Identity: 47% PDB header:transcription Chain: A: PDB Molecule:histone deacetylase complex subunit sap30; PDBTitle: solution structure of the msin3a pah3-sap30 sid complex Phyre2 PDB 3mqp chain B Region: 72 - 82 Aligned: 11 Modelled: 11 Confidence: 11.5% Identity: 73% PDB header:apoptosis Chain: B: PDB Molecule:phorbol-12-myristate-13-acetate-induced protein 1; PDBTitle: crystal structure of human bfl-1 in complex with noxa bh3 peptide,2 northeast structural genomics consortium target hr2930 Phyre2 PDB 3kzw chain D Region: 118 - 153 Aligned: 36 Modelled: 36 Confidence: 8.1% Identity: 22% PDB header:hydrolase Chain: D: PDB Molecule:cytosol aminopeptidase; PDBTitle: crystal structure of cytosol aminopeptidase from staphylococcus aureus2 col Phyre2 PDB 2eqo chain A Region: 30 - 37 Aligned: 8 Modelled: 8 Confidence: 8.0% Identity: 63% PDB header:transcription Chain: A: PDB Molecule:tnf receptor-associated factor 3-interacting PDBTitle: solution structure of the stn_traf3ip1_nd domain of2 interleukin 13 receptor alpha 1-binding protein-1 [homo3 sapiens] Phyre2 PDB 1sg1 chain X domain 2 Region: 14 - 21 Aligned: 8 Modelled: 8 Confidence: 8.0% Identity: 63% Fold: TNF receptor-like Superfamily: TNF receptor-like Family: TNF receptor-like Phyre2 PDB 1j3b chain A domain 2 Region: 54 - 124 Aligned: 71 Modelled: 71 Confidence: 7.0% Identity: 21% Fold: PEP carboxykinase N-terminal domain Superfamily: PEP carboxykinase N-terminal domain Family: PEP carboxykinase N-terminal domain Phyre2 PDB 3im0 chain A Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 6.3% Identity: 19% PDB header:lyase Chain: A: PDB Molecule:val-1; PDBTitle: crystal structure of chlorella virus val-1 soaked in 200mm d-2 glucuronic acid, 10% peg-3350, and 200mm glycine-naoh (ph 10.0) Phyre2 PDB 2iif chain A Region: 94 - 108 Aligned: 15 Modelled: 15 Confidence: 6.0% Identity: 40% PDB header:recombination/dna Chain: A: PDB Molecule:integration host factor; PDBTitle: single chain integration host factor mutant protein (scihf2-2 k45ae) in complex with dna Phyre2 PDB 1w4m chain A Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 5.8% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: DEP domain Phyre2 PDB 2cso chain A domain 1 Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 5.7% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: DEP domain Phyre2 PDB 3hlu chain A Region: 108 - 128 Aligned: 21 Modelled: 21 Confidence: 5.6% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein duf2179; PDBTitle: crystal structure of uncharacterized protein conserved in bacteria2 duf2179 from eubacterium ventriosum Phyre2 PDB 1lan chain A Region: 118 - 153 Aligned: 36 Modelled: 36 Confidence: 5.6% Identity: 19% PDB header:hydrolase (alpha-aminoacylpeptide) Chain: A: PDB Molecule:leucine aminopeptidase; PDBTitle: leucine aminopeptidase complex with l-leucinal Phyre2 PDB 1kjs chain A Region: 130 - 138 Aligned: 9 Modelled: 9 Confidence: 5.6% Identity: 33% Fold: Anaphylotoxins (complement system) Superfamily: Anaphylotoxins (complement system) Family: Anaphylotoxins (complement system) Phyre2 PDB 1gxi chain E Region: 133 - 147 Aligned: 15 Modelled: 15 Confidence: 5.5% Identity: 60% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: Photosystem I accessory protein E (PsaE) Phyre2 PDB 1pse chain A Region: 133 - 147 Aligned: 15 Modelled: 15 Confidence: 5.4% Identity: 60% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: Photosystem I accessory protein E (PsaE) Phyre2 PDB 1k8r chain B Region: 18 - 28 Aligned: 11 Modelled: 11 Confidence: 5.4% Identity: 64% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ras-binding domain, RBD Phyre2 1 c2nr1A_ 2 d1ffgb_ 3 c1a0oH_ 4 c2ysrA_ 5 c2ld7A_ 6 c3mqpB_ 7 c3kzwD_ 8 c2eqoA_ 9 d1sg1x2 10 d1j3ba2 11 c3im0A_ 12 c2iifA_ 13 d1w4ma_ 14 d2csoa1 15 c3hluA_ 16 c1lanA_ 17 d1kjsa_ 18 d1gxie_ 19 d1psea_ 20 d1k8rb_ 21 22

Detailed template information

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

1 c2nr1A_ 18.1 80 PDB header:receptor Chain: A: PDB Molecule:nr1 m2; PDBTitle: transmembrane segment 2 of nmda receptor nr1, nmr, 102 structures 2 d1ffgb_ 17.9 57 Fold:Ferredoxin-like Superfamily:CheY-binding domain of CheA Family:CheY-binding domain of CheA 3 c1a0oH_ 17.7 57 PDB header:chemotaxis Chain: H: PDB Molecule:chea; PDBTitle: chey-binding domain of chea in complex with chey 4 c2ysrA_ 13.4 20 PDB header:signaling protein Chain: A: PDB Molecule:dep domain-containing protein 1; PDBTitle: solution structure of the dep domain from human dep domain-2 containing protein 1 5 c2ld7A_ 11.6 47 PDB header:transcription Chain: A: PDB Molecule:histone deacetylase complex subunit sap30; PDBTitle: solution structure of the msin3a pah3-sap30 sid complex 6 c3mqpB_ 11.5 73 PDB header:apoptosis Chain: B: PDB Molecule:phorbol-12-myristate-13-acetate-induced protein 1; PDBTitle: crystal structure of human bfl-1 in complex with noxa bh3 peptide,2 northeast structural genomics consortium target hr2930 7 c3kzwD_ 8.1 22 PDB header:hydrolase Chain: D: PDB Molecule:cytosol aminopeptidase; PDBTitle: crystal structure of cytosol aminopeptidase from staphylococcus aureus2 col 8 c2eqoA_ 8.0 63 PDB header:transcription Chain: A: PDB Molecule:tnf receptor-associated factor 3-interacting PDBTitle: solution structure of the stn_traf3ip1_nd domain of2 interleukin 13 receptor alpha 1-binding protein-1 [homo3 sapiens] 9 d1sg1x2 8.0 63 Fold:TNF receptor-like Superfamily:TNF receptor-like Family:TNF receptor-like 10 d1j3ba2 7.0 21 Fold:PEP carboxykinase N-terminal domain Superfamily:PEP carboxykinase N-terminal domain Family:PEP carboxykinase N-terminal domain 11 c3im0A_ 6.3 19 PDB header:lyase Chain: A: PDB Molecule:val-1; PDBTitle: crystal structure of chlorella virus val-1 soaked in 200mm d-2 glucuronic acid, 10% peg-3350, and 200mm glycine-naoh (ph 10.0) 12 c2iifA_ 6.0 40 PDB header:recombination/dna Chain: A: PDB Molecule:integration host factor; PDBTitle: single chain integration host factor mutant protein (scihf2-2 k45ae) in complex with dna 13 d1w4ma_ 5.8 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain 14 d2csoa1 5.7 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain 15 c3hluA_ 5.6 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein duf2179; PDBTitle: crystal structure of uncharacterized protein conserved in bacteria2 duf2179 from eubacterium ventriosum 16 c1lanA_ 5.6 19 PDB header:hydrolase (alpha-aminoacylpeptide) Chain: A: PDB Molecule:leucine aminopeptidase; PDBTitle: leucine aminopeptidase complex with l-leucinal 17 d1kjsa_ 5.6 33 Fold:Anaphylotoxins (complement system) Superfamily:Anaphylotoxins (complement system) Family:Anaphylotoxins (complement system) 18 d1gxie_ 5.5 60 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:Photosystem I accessory protein E (PsaE) 19 d1psea_ 5.4 60 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:Photosystem I accessory protein E (PsaE) 20 d1k8rb_ 5.4 64 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ras-binding domain, RBD 21 d2o0qa1 not modelled 5.4 40 Fold:ADP-ribosylation Superfamily:ADP-ribosylation Family:CC0527-like 22 d1evsa_ not modelled 5.3 24 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Long-chain cytokines

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