Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	N	P	N	P	K	R	S	D	E	P	V	F	W	G	L	F	G	A	G	G	M	W	S	A	I	I	A	P	V	M	I	L	L	V	G	I	L	L	P	L	G	L	F	P	G	D	A	L	S	Y	E	R	V	L	A	F	A	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.
Sequence		S	F	I	G	R	V	F	L	F	L	M	I	V	L	P	L	W	C	G	L	H	R	M	H	H	A	M	H	D	L	K	I	H	V	P	A	G	K	W	V	F	Y	G	L	A	A	I	L	T	V	V	T	L	I	G	V	V	T	I
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 1kf6 chain D Region: 1 - 119 Aligned: 119 Modelled: 119 Confidence: 100.0% Identity: 100% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1nek chain D Region: 28 - 119 Aligned: 91 Modelled: 92 Confidence: 96.1% Identity: 19% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1nek chain C Region: 1 - 116 Aligned: 114 Modelled: 116 Confidence: 96.1% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1kf6 chain C Region: 28 - 117 Aligned: 90 Modelled: 90 Confidence: 74.3% Identity: 17% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1yq3 chain C Region: 32 - 119 Aligned: 88 Modelled: 88 Confidence: 26.7% Identity: 10% PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone Phyre2 PDB 1v54 chain M Region: 19 - 54 Aligned: 32 Modelled: 36 Confidence: 23.7% Identity: 16% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Phyre2 PDB 3kdp chain H Region: 94 - 113 Aligned: 20 Modelled: 20 Confidence: 18.5% Identity: 35% 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: 94 - 113 Aligned: 20 Modelled: 20 Confidence: 18.5% Identity: 35% 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 2y69 chain Z Region: 19 - 54 Aligned: 32 Modelled: 36 Confidence: 16.6% Identity: 16% PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1kwi chain A Region: 4 - 17 Aligned: 14 Modelled: 14 Confidence: 10.9% Identity: 21% Fold: Cystatin-like Superfamily: Cystatin/monellin Family: Cathelicidin motif Phyre2 PDB 2jo1 chain A Region: 24 - 42 Aligned: 19 Modelled: 19 Confidence: 7.6% Identity: 21% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 2bh1 chain A domain 2 Region: 6 - 22 Aligned: 17 Modelled: 17 Confidence: 7.2% Identity: 12% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Cyto-EpsL domain Phyre2 PDB 3ez3 chain A Region: 2 - 26 Aligned: 25 Modelled: 25 Confidence: 6.7% Identity: 8% PDB header:lyase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase, putative; PDBTitle: crystal structure of plasmodium vivax geranylgeranylpyrophosphate2 synthase pvx_092040 with zoledronate and ipp bound Phyre2 PDB 3db3 chain A Region: 1 - 15 Aligned: 15 Modelled: 14 Confidence: 6.2% Identity: 40% PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide Phyre2 PDB 3lsn chain A Region: 2 - 26 Aligned: 25 Modelled: 24 Confidence: 5.5% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of putative geranyltranstransferase from pseudomonas2 fluorescens pf-5 complexed with magnesium Phyre2 PDB 2jp3 chain A Region: 24 - 42 Aligned: 19 Modelled: 19 Confidence: 5.4% Identity: 26% 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 1 d1kf6d_ 2 d1nekd_ 3 d1nekc_ 4 d1kf6c_ 5 c1yq3C_ 6 d1v54m_ 7 c3kdpH_ 8 c3kdpG_ 9 c2y69Z_ 10 d1kwia_ 11 c2jo1A_ 12 d2bh1a2 13 c3ez3A_ 14 c3db3A_ 15 c3lsnA_ 16 c2jp3A_

Detailed template information

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

1 d1kf6d_ 100.0 100 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 2 d1nekd_ 96.1 19 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 3 d1nekc_ 96.1 15 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 4 d1kf6c_ 74.3 17 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 5 c1yq3C_ 26.7 10 PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone 6 d1v54m_ 23.7 16 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) 7 c3kdpH_ 18.5 35 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 8 c3kdpG_ 18.5 35 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 9 c2y69Z_ 16.6 16 PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 10 d1kwia_ 10.9 21 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:Cathelicidin motif 11 c2jo1A_ 7.6 21 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 12 d2bh1a2 7.2 12 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Cyto-EpsL domain 13 c3ez3A_ 6.7 8 PDB header:lyase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase, putative; PDBTitle: crystal structure of plasmodium vivax geranylgeranylpyrophosphate2 synthase pvx_092040 with zoledronate and ipp bound 14 c3db3A_ 6.2 40 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide 15 c3lsnA_ 5.5 16 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of putative geranyltranstransferase from pseudomonas2 fluorescens pf-5 complexed with magnesium 16 c2jp3A_ 5.4 26 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

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

---

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