Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	H	E	I	T	L	L	Q	G	L	S	L	A	A	L	V	F	V	L	G	I	D	F	W	L	E	A	L	F	L	F	R	P	I	I	V	C	T	L	T	G	A	I	L	G	D	I	Q	T	G	L	I	T	G	G	L	T	E	L	A
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	A	G	L	T	P	A	G	G	V	Q	P	P	N	P	I	M	A	G	L	M	T	T	V	I	A	W	S	T	G	V	D	A	K	T	A	I	G	L	G	L	P	F	S	L	L	M	Q	Y	V	I	L	F	F	Y	S	A	F	S	L
Secondary structure
SS confidence
Disorder							?	?																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	M	T	K	A	D	K	C	A	K	E	A	D	T	A	A	F	S	R	L	N	W	T	T	M	L	I	V	A	S	A	Y	A	V	I	A	F	L	C	T	Y	L	A	Q	G	A	M	Q	A	L	V	K	A	M	P	A	W	L	T	H
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	F	E	V	A	G	G	I	L	P	A	V	G	F	G	L	L	L	R	V	M	F	K	A	Q	Y	I	P	Y	L	I	A	G	F	L	F	V	C	Y	I	Q	V	S	N	L	L	P	V	A	V	L	G	A	G	F	A	V	Y	E	F
Secondary structure
SS confidence
Disorder																																										?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.
Sequence		F	N	A	K	S	R	Q	Q	A	Q	P	Q	P	V	A	S	K	N	E	E	E	D	Y	S	N	G	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 3qnq chain D Region: 207 - 261 Aligned: 55 Modelled: 55 Confidence: 38.0% Identity: 18% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 2l34 chain B Region: 31 - 65 Aligned: 33 Modelled: 34 Confidence: 32.0% Identity: 18% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 PDB 2kdx chain A Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 31.0% Identity: 36% PDB header:metal-binding protein Chain: A: PDB Molecule:hydrogenase/urease nickel incorporation protein PDBTitle: solution structure of hypa protein Phyre2 PDB 2l35 chain B Region: 31 - 57 Aligned: 27 Modelled: 27 Confidence: 29.4% Identity: 15% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer Phyre2 PDB 1cii chain A Region: 70 - 121 Aligned: 51 Modelled: 52 Confidence: 23.6% Identity: 18% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 3mku chain A Region: 74 - 255 Aligned: 182 Modelled: 182 Confidence: 22.8% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter Phyre2 PDB 2l34 chain A Region: 31 - 57 Aligned: 27 Modelled: 27 Confidence: 20.5% Identity: 15% PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 PDB 2eel chain A Region: 252 - 265 Aligned: 14 Modelled: 14 Confidence: 19.3% Identity: 7% PDB header:apoptosis Chain: A: PDB Molecule:cell death activator cide-a; PDBTitle: solution structure of the cide-n domain of human cell death2 activator cide-a Phyre2 PDB 1ibx chain B Region: 252 - 264 Aligned: 13 Modelled: 13 Confidence: 15.4% Identity: 15% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: CAD domain Phyre2 PDB 1ibx chain B Region: 252 - 264 Aligned: 13 Modelled: 13 Confidence: 15.4% Identity: 15% PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:chimera of igg binding protein g and dna PDBTitle: nmr structure of dff40 and dff45 n-terminal domain complex Phyre2 PDB 1d4b chain A Region: 252 - 264 Aligned: 13 Modelled: 13 Confidence: 14.8% Identity: 15% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: CAD domain Phyre2 PDB 2l35 chain A Region: 37 - 66 Aligned: 28 Modelled: 30 Confidence: 14.0% Identity: 21% PDB header:protein binding Chain: A: PDB Molecule:dap12-nkg2c_tm; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer Phyre2 PDB 1f2r chain I Region: 252 - 265 Aligned: 14 Modelled: 14 Confidence: 12.6% Identity: 14% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: CAD domain Phyre2 PDB 1iwg chain A domain 8 Region: 79 - 185 Aligned: 107 Modelled: 107 Confidence: 10.5% Identity: 7% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1fft chain C Region: 109 - 154 Aligned: 46 Modelled: 46 Confidence: 9.1% Identity: 15% Fold: Cytochrome c oxidase subunit III-like Superfamily: Cytochrome c oxidase subunit III-like Family: Cytochrome c oxidase subunit III-like Phyre2 PDB 1v54 chain I Region: 215 - 264 Aligned: 50 Modelled: 50 Confidence: 7.2% Identity: 16% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIc Family: Mitochondrial cytochrome c oxidase subunit VIc Phyre2 PDB 1eys chain H domain 2 Region: 219 - 249 Aligned: 31 Modelled: 31 Confidence: 7.1% Identity: 13% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 2jo1 chain A Region: 225 - 267 Aligned: 43 Modelled: 43 Confidence: 6.8% Identity: 12% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 2ko6 chain A Region: 236 - 263 Aligned: 28 Modelled: 28 Confidence: 6.5% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929 Phyre2 PDB 1r7m chain A domain 1 Region: 33 - 46 Aligned: 14 Modelled: 14 Confidence: 5.7% Identity: 36% Fold: Homing endonuclease-like Superfamily: Homing endonucleases Family: Group I mobile intron endonuclease Phyre2 1 c3qnqD_ 2 c2l34B_ 3 c2kdxA_ 4 c2l35B_ 5 c1ciiA_ 6 c3mkuA_ 7 c2l34A_ 8 c2eelA_ 9 d1ibxb_ 10 c1ibxB_ 11 d1d4ba_ 12 c2l35A_ 13 d1f2ri_ 14 d1iwga8 15 d1fftc_ 16 d1v54i_ 17 d1eysh2 18 c2jo1A_ 19 c2ko6A_ 20 d1r7ma1 21

Detailed template information

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

1 c3qnqD_ 38.0 18 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 2 c2l34B_ 32.0 18 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 3 c2kdxA_ 31.0 36 PDB header:metal-binding protein Chain: A: PDB Molecule:hydrogenase/urease nickel incorporation protein PDBTitle: solution structure of hypa protein 4 c2l35B_ 29.4 15 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer 5 c1ciiA_ 23.6 18 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 6 c3mkuA_ 22.8 12 PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter 7 c2l34A_ 20.5 15 PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 8 c2eelA_ 19.3 7 PDB header:apoptosis Chain: A: PDB Molecule:cell death activator cide-a; PDBTitle: solution structure of the cide-n domain of human cell death2 activator cide-a 9 d1ibxb_ 15.4 15 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:CAD domain 10 c1ibxB_ 15.4 15 PDB header:hydrolase/hydrolase inhibitor Chain: B: PDB Molecule:chimera of igg binding protein g and dna PDBTitle: nmr structure of dff40 and dff45 n-terminal domain complex 11 d1d4ba_ 14.8 15 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:CAD domain 12 c2l35A_ 14.0 21 PDB header:protein binding Chain: A: PDB Molecule:dap12-nkg2c_tm; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer 13 d1f2ri_ 12.6 14 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:CAD domain 14 d1iwga8 10.5 7 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 15 d1fftc_ 9.1 15 Fold:Cytochrome c oxidase subunit III-like Superfamily:Cytochrome c oxidase subunit III-like Family:Cytochrome c oxidase subunit III-like 16 d1v54i_ 7.2 16 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIc Family:Mitochondrial cytochrome c oxidase subunit VIc 17 d1eysh2 7.1 13 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 18 c2jo1A_ 6.8 12 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 19 c2ko6A_ 6.5 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929 20 d1r7ma1 5.7 36 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Group I mobile intron endonuclease 21 c3fseB_ not modelled 5.4 88 PDB header:hydrolase Chain: B: PDB Molecule:two-domain protein containing dj-1/thij/pfpi-like and PDBTitle: crystal structure of a two-domain protein containing dj-1/thij/pfpi-2 like and ferritin-like domains (ava_4496) from anabaena variabilis3 atcc 29413 at 1.90 a resolution

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