Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	T	K	R	K	P	Y	V	R	P	M	T	S	T	W	W	K	K	L	P	F	Y	R	F	Y	M	L	R	E	G	T	A	V	P	A	V	W	F	S	I	E	L	I	F	G	L	F	A	L	K	N	G	P	E	A	W	A	G	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	D	F	L	Q	N	P	V	I	V	I	I	N	L	I	T	L	A	A	A	L	L	H	T	K	T	W	F	E	L	A	P	K	A	A	N	I	I	V	K	D	E	K	M	G	P	E	P	I	I	K	S	L	W	A	V	T	V	V	A
Secondary structure
SS confidence
Disorder																																								?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.
Sequence		T	I	V	I	L	F	V	A	L	Y	W
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 C Region: 2 - 131 Aligned: 130 Modelled: 130 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: 24 - 130 Aligned: 97 Modelled: 107 Confidence: 96.8% Identity: 20% 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: 28 - 130 Aligned: 96 Modelled: 103 Confidence: 89.7% 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 D Region: 32 - 129 Aligned: 89 Modelled: 98 Confidence: 75.1% 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: 28 - 129 Aligned: 97 Modelled: 102 Confidence: 68.7% Identity: 13% PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone Phyre2 PDB 2bs2 chain C domain 1 Region: 18 - 130 Aligned: 113 Modelled: 113 Confidence: 32.7% Identity: 12% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Fumarate reductase respiratory complex cytochrome b subunit, FrdC Phyre2 PDB 2b1w chain A Region: 51 - 70 Aligned: 20 Modelled: 20 Confidence: 26.6% Identity: 30% PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain protein 4; PDBTitle: solution structure of the nod1 caspase activating and recruitment2 domain Phyre2 PDB 1lg7 chain A Region: 19 - 29 Aligned: 11 Modelled: 11 Confidence: 23.7% Identity: 36% Fold: VSV matrix protein Superfamily: VSV matrix protein Family: VSV matrix protein Phyre2 PDB 2w2r chain A Region: 19 - 29 Aligned: 11 Modelled: 11 Confidence: 20.5% Identity: 45% PDB header:viral protein Chain: A: PDB Molecule:matrix protein; PDBTitle: structure of the vesicular stomatitis virus matrix protein Phyre2 PDB 3ygs chain P Region: 51 - 66 Aligned: 16 Modelled: 16 Confidence: 20.0% Identity: 25% Fold: DEATH domain Superfamily: DEATH domain Family: Caspase recruitment domain, CARD Phyre2 PDB 2nz7 chain A Region: 51 - 65 Aligned: 15 Modelled: 15 Confidence: 19.0% Identity: 33% PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain-containing protein 4; PDBTitle: crystal structure analysis of caspase-recruitment domain2 (card) of nod1 Phyre2 PDB 3kat chain A Region: 51 - 65 Aligned: 15 Modelled: 15 Confidence: 17.5% Identity: 13% PDB header:apoptosis Chain: A: PDB Molecule:nacht, lrr and pyd domains-containing protein 1; PDBTitle: crystal structure of the card domain of the human nlrp12 protein, northeast structural genomics consortium target3 hr3486e Phyre2 PDB 3crd chain A Region: 51 - 66 Aligned: 16 Modelled: 16 Confidence: 15.4% Identity: 44% Fold: DEATH domain Superfamily: DEATH domain Family: Caspase recruitment domain, CARD Phyre2 PDB 1dgn chain A Region: 51 - 66 Aligned: 16 Modelled: 16 Confidence: 14.1% Identity: 25% Fold: DEATH domain Superfamily: DEATH domain Family: Caspase recruitment domain, CARD Phyre2 PDB 2kxw chain B Region: 21 - 29 Aligned: 9 Modelled: 9 Confidence: 13.5% Identity: 44% PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2 Phyre2 PDB 1y9b chain A domain 1 Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 12.7% Identity: 20% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: VCA0319-like Phyre2 PDB 1p58 chain F Region: 15 - 46 Aligned: 32 Modelled: 32 Confidence: 11.8% Identity: 16% PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction Phyre2 PDB 2q0o chain C Region: 50 - 67 Aligned: 18 Modelled: 18 Confidence: 10.9% Identity: 11% PDB header:transcription Chain: C: PDB Molecule:probable transcriptional repressor tram; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing Phyre2 PDB 2h3o chain A Region: 41 - 81 Aligned: 37 Modelled: 41 Confidence: 9.9% Identity: 24% PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices Phyre2 PDB 1cy5 chain A Region: 51 - 66 Aligned: 16 Modelled: 16 Confidence: 9.7% Identity: 19% Fold: DEATH domain Superfamily: DEATH domain Family: Caspase recruitment domain, CARD Phyre2 1 d1kf6c_ 2 d1nekd_ 3 d1nekc_ 4 d1kf6d_ 5 c1yq3C_ 6 d2bs2c1 7 c2b1wA_ 8 d1lg7a_ 9 c2w2rA_ 10 d3ygsp_ 11 c2nz7A_ 12 c3katA_ 13 d3crda_ 14 d1dgna_ 15 c2kxwB_ 16 d1y9ba1 17 c1p58F_ 18 c2q0oC_ 19 c2h3oA_ 20 d1cy5a_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 d1kf6c_ 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_ 96.8 20 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_ 89.7 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 d1kf6d_ 75.1 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_ 68.7 13 PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone 6 d2bs2c1 32.7 12 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Fumarate reductase respiratory complex cytochrome b subunit, FrdC 7 c2b1wA_ 26.6 30 PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain protein 4; PDBTitle: solution structure of the nod1 caspase activating and recruitment2 domain 8 d1lg7a_ 23.7 36 Fold:VSV matrix protein Superfamily:VSV matrix protein Family:VSV matrix protein 9 c2w2rA_ 20.5 45 PDB header:viral protein Chain: A: PDB Molecule:matrix protein; PDBTitle: structure of the vesicular stomatitis virus matrix protein 10 d3ygsp_ 20.0 25 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 11 c2nz7A_ 19.0 33 PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain-containing protein 4; PDBTitle: crystal structure analysis of caspase-recruitment domain2 (card) of nod1 12 c3katA_ 17.5 13 PDB header:apoptosis Chain: A: PDB Molecule:nacht, lrr and pyd domains-containing protein 1; PDBTitle: crystal structure of the card domain of the human nlrp12 protein, northeast structural genomics consortium target3 hr3486e 13 d3crda_ 15.4 44 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 14 d1dgna_ 14.1 25 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 15 c2kxwB_ 13.5 44 PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2 16 d1y9ba1 12.7 20 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VCA0319-like 17 c1p58F_ 11.8 16 PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 18 c2q0oC_ 10.9 11 PDB header:transcription Chain: C: PDB Molecule:probable transcriptional repressor tram; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 19 c2h3oA_ 9.9 24 PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices 20 d1cy5a_ 9.7 19 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 21 d1bw6a_ not modelled 9.5 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 22 c1wazA_ not modelled 8.4 24 PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles 23 d2axtk1 not modelled 7.9 38 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein K, PsbK Family:PsbK-like 24 c2y69W_ not modelled 7.1 19 PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 25 d1kcfa2 not modelled 7.0 23 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Mitochondrial resolvase ydc2 catalytic domain 26 c2voyB_ not modelled 6.9 15 PDB header:hydrolase Chain: B: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 27 c1kcfB_ not modelled 6.0 23 PDB header:hydrolase Chain: B: PDB Molecule:hypothetical 30.2 kd protein c25g10.02 in PDBTitle: crystal structure of the yeast mitochondrial holliday2 junction resolvase, ydc2 28 c2l9mA_ not modelled 5.9 28 PDB header:apoptosis inhibitor Chain: A: PDB Molecule:baculoviral iap repeat-containing protein 2; PDBTitle: structure of ciap1 card 29 d1ic8a2 not modelled 5.9 30 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 30 c2zidA_ not modelled 5.4 42 PDB header:hydrolase Chain: A: PDB Molecule:dextran glucosidase; PDBTitle: crystal structure of dextran glucosidase e236q complex with2 isomaltotriose

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