Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	Q	Y	L	N	V	F	F	Y	D	I	Y	P	Y	I	C	A	T	V	F	F	L	G	S	W	L	R	Y	D	Y	G	Q	Y	T	W	R	A	S	S	S	Q	M	L	D	K	R	G	M	V	I	W	S	N	L	F	H	I	G	I
Secondary structure
SS confidence
Disorder		?	?	?																														?	?						?							?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	G	I	F	F	G	H	L	F	G	M	L	T	P	H	W	M	Y	A	W	F	L	P	V	A	A	K	Q	L	M	A	M	V	L	G	G	I	C	G	V	L	T	L	I	G	G	A	G	L	L	W	R	R	L	T	N	Q	R	V	R
Secondary structure
SS confidence
Disorder																																																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	T	S	T	T	P	D	I	I	I	M	S	I	L	L	I	Q	C	L	L	G	L	S	T	I	P	F	S	A	Q	Y	P	D	G	S	E	M	M	K	L	V	G	W	A	Q	S	I	V	T	F	R	G	G	S	S	E	M	L	N	G
Secondary structure
SS confidence
Disorder		?																																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.
Sequence		V	A	F	V	F	R	L	H	L	V	L	G	M	T	I	F	L	L	F	P	F	T	R	L	V	H	V	W	S	A	P	F	E	Y	F	T	R	R	Y	Q	I	V	R	S	R	R
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 1y5i chain C domain 1 Region: 3 - 225 Aligned: 215 Modelled: 223 Confidence: 100.0% Identity: 72% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 2knc chain A Region: 92 - 127 Aligned: 36 Modelled: 36 Confidence: 75.6% Identity: 22% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2klu chain A Region: 92 - 123 Aligned: 32 Modelled: 32 Confidence: 71.7% Identity: 34% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 1kqf chain C Region: 55 - 200 Aligned: 123 Modelled: 123 Confidence: 57.7% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Formate dehydrogenase N, cytochrome (gamma) subunit Phyre2 PDB 2k1a chain A Region: 92 - 120 Aligned: 29 Modelled: 29 Confidence: 39.1% Identity: 24% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 3kdp chain H Region: 97 - 113 Aligned: 17 Modelled: 17 Confidence: 38.9% Identity: 24% PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 3kdp chain G Region: 97 - 113 Aligned: 17 Modelled: 17 Confidence: 38.9% Identity: 24% PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 2w8a chain C Region: 5 - 168 Aligned: 156 Modelled: 163 Confidence: 18.2% Identity: 11% PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate Phyre2 PDB 2jp3 chain A Region: 87 - 124 Aligned: 38 Modelled: 38 Confidence: 13.0% Identity: 18% PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles Phyre2 PDB 2k1l chain B Region: 87 - 113 Aligned: 27 Modelled: 27 Confidence: 11.9% Identity: 26% PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 Phyre2 PDB 2k1k chain B Region: 87 - 113 Aligned: 27 Modelled: 27 Confidence: 11.9% Identity: 26% PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 Phyre2 PDB 2k1l chain A Region: 87 - 113 Aligned: 27 Modelled: 27 Confidence: 11.9% Identity: 26% PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 Phyre2 PDB 2k1k chain A Region: 87 - 113 Aligned: 27 Modelled: 27 Confidence: 11.9% Identity: 26% PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 Phyre2 PDB 2k9y chain B Region: 83 - 113 Aligned: 31 Modelled: 31 Confidence: 10.2% Identity: 26% PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 2jo1 chain A Region: 87 - 117 Aligned: 31 Modelled: 31 Confidence: 9.8% Identity: 26% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 2k9y chain A Region: 83 - 113 Aligned: 31 Modelled: 31 Confidence: 7.5% Identity: 26% PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 2dyo chain B Region: 109 - 120 Aligned: 12 Modelled: 12 Confidence: 6.7% Identity: 50% PDB header:protein turnover/protein turnover Chain: B: PDB Molecule:autophagy protein 16; PDBTitle: the crystal structure of saccharomyces cerevisiae atg5-2 atg16(1-57) complex Phyre2 PDB 1ar1 chain A Region: 44 - 123 Aligned: 80 Modelled: 80 Confidence: 5.6% Identity: 16% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 1 d1y5ic1 2 c2kncA_ 3 c2kluA_ 4 d1kqfc_ 5 c2k1aA_ 6 c3kdpH_ 7 c3kdpG_ 8 c2w8aC_ 9 c2jp3A_ 10 c2k1lB_ 11 c2k1kB_ 12 c2k1lA_ 13 c2k1kA_ 14 c2k9yB_ 15 c2jo1A_ 16 c2k9yA_ 17 c2dyoB_ 18 d1ar1a_

Detailed template information

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

1 d1y5ic1 100.0 72 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 2 c2kncA_ 75.6 22 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 3 c2kluA_ 71.7 34 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 4 d1kqfc_ 57.7 15 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 5 c2k1aA_ 39.1 24 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 6 c3kdpH_ 38.9 24 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 7 c3kdpG_ 38.9 24 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 8 c2w8aC_ 18.2 11 PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate 9 c2jp3A_ 13.0 18 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 10 c2k1lB_ 11.9 26 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 11 c2k1kB_ 11.9 26 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 12 c2k1lA_ 11.9 26 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 13 c2k1kA_ 11.9 26 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 14 c2k9yB_ 10.2 26 PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 15 c2jo1A_ 9.8 26 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 16 c2k9yA_ 7.5 26 PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 17 c2dyoB_ 6.7 50 PDB header:protein turnover/protein turnover Chain: B: PDB Molecule:autophagy protein 16; PDBTitle: the crystal structure of saccharomyces cerevisiae atg5-2 atg16(1-57) complex 18 d1ar1a_ 5.6 16 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-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