Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	I	M	R	S	V	V	G	M	V	V	L	L	A	I	A	F	L	L	S	V	N	K	K	S	I	S	L	R	T	V	G	A	A	L	L	L	Q	I	A	I	G	G	I	M	L	Y	F	P	P	G	K	W	A	V	E	Q	A	A
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	G	V	H	K	V	M	S	Y	S	D	A	G	S	A	F	I	F	G	S	L	V	G	P	K	M	D	V	L	F	D	G	A	G	F	I	F	A	F	R	V	L	P	A	I	I	F	V	T	A	L	I	S	L	L	Y	Y	I	G	V
Secondary structure
SS confidence
Disorder																								?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	G	L	L	I	R	I	L	G	S	I	F	Q	K	A	L	N	I	S	K	I	E	S	F	V	A	V	T	T	I	F	L	G	Q	N	E	I	P	A	I	V	K	P	F	I	D	R	M	N	R	N	E	L	F	T	A	I	C	S	G
Secondary structure
SS confidence
Disorder																		?			?	?	?	?													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		M	A	S	I	A	G	S	M	M	I	G	Y	A	G	M	G	V	P	I	D	Y	L	L	A	A	S	L	M	A	I	P	G	G	I	L	F	A	R	I	L	S	P	A	T	E	P	S	Q	V	T	F	E	N	L	S	F	S	E	T	P
Secondary structure
SS confidence
Disorder																																															?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		P	K	S	F	I	E	A	A	A	S	G	A	M	T	G	L	K	I	A	A	G	V	A	T	V	V	M	A	F	V	A	I	I	A	L	I	N	G	I	I	G	G	I	G	G	W	F	G	F	A	N	A	S	L	E	S	I	F	G	Y
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	L	A	P	L	A	W	I	M	G	V	D	W	S	D	A	N	L	A	G	S	L	I	G	Q	K	L	A	I	N	E	F	V	A	Y	L	S	F	S	P	Y	L	Q	T	G	G	T	L	E	V	K	T	I	A	I	I	S	F	A	L
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.
Sequence		C	G	F	A	N	F	G	S	I	G	V	V	V	G	A	F	S	A	I	S	P	K	R	A	P	E	I	A	Q	L	G	L	R	A	L	A	A	A	T	L	S	N	L	M	S	A	T	I	A	G	F	F	I	G	L	A
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 1bct chain A Region: 296 - 312 Aligned: 17 Modelled: 17 Confidence: 47.7% Identity: 18% PDB header:photoreceptor Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: three-dimensional structure of proteolytic fragment 163-2312 of bacterioopsin determined from nuclear magnetic3 resonance data in solution Phyre2 PDB 2r6g chain F domain 1 Region: 2 - 52 Aligned: 50 Modelled: 50 Confidence: 37.0% Identity: 12% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 2l2t chain A Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 18.8% Identity: 24% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain Phyre2 PDB 1z21 chain A domain 1 Region: 161 - 176 Aligned: 16 Modelled: 16 Confidence: 18.2% Identity: 19% Fold: Type III secretion system domain Superfamily: Type III secretion system domain Family: YopR Core Phyre2 PDB 2i2x chain O Region: 361 - 398 Aligned: 33 Modelled: 38 Confidence: 16.9% Identity: 24% PDB header:transferase Chain: O: PDB Molecule:methyltransferase 1; PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri Phyre2 PDB 1tm9 chain A Region: 89 - 121 Aligned: 31 Modelled: 33 Confidence: 12.7% Identity: 32% Fold: Hypothetical protein MG354 Superfamily: Hypothetical protein MG354 Family: Hypothetical protein MG354 Phyre2 PDB 3a7k chain D Region: 297 - 312 Aligned: 16 Modelled: 16 Confidence: 12.7% Identity: 25% PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis Phyre2 PDB 1e12 chain A Region: 297 - 310 Aligned: 14 Modelled: 14 Confidence: 12.2% Identity: 21% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 2jag chain A Region: 297 - 310 Aligned: 14 Modelled: 14 Confidence: 11.8% Identity: 21% PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v Phyre2 PDB 3ddl chain B Region: 296 - 324 Aligned: 29 Modelled: 29 Confidence: 11.1% Identity: 10% PDB header:transport protein Chain: B: PDB Molecule:xanthorhodopsin; PDBTitle: crystallographic structure of xanthorhodopsin, a light-2 driven ion pump with dual chromophore Phyre2 PDB 1uaz chain A Region: 296 - 312 Aligned: 17 Modelled: 17 Confidence: 9.9% Identity: 24% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 1vke chain B Region: 334 - 360 Aligned: 27 Modelled: 27 Confidence: 9.9% Identity: 19% Fold: AhpD-like Superfamily: AhpD-like Family: CMD-like Phyre2 PDB 3am6 chain C Region: 296 - 310 Aligned: 15 Modelled: 15 Confidence: 9.6% Identity: 27% PDB header:transport protein Chain: C: PDB Molecule:rhodopsin-2; PDBTitle: crystal structure of the proton pumping rhodopsin ar2 from marine alga2 acetabularia acetabulum Phyre2 PDB 1h2s chain A Region: 297 - 310 Aligned: 14 Modelled: 14 Confidence: 9.5% Identity: 21% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 2axt chain I domain 1 Region: 74 - 92 Aligned: 19 Modelled: 19 Confidence: 9.3% Identity: 26% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein I, PsbI Family: PsbI-like Phyre2 PDB 1xio chain A Region: 297 - 312 Aligned: 16 Modelled: 16 Confidence: 9.2% Identity: 25% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 1xio chain A Region: 297 - 312 Aligned: 16 Modelled: 16 Confidence: 9.2% Identity: 25% PDB header:signaling protein Chain: A: PDB Molecule:anabaena sensory rhodopsin; PDBTitle: anabaena sensory rhodopsin Phyre2 PDB 1m0k chain A Region: 296 - 312 Aligned: 17 Modelled: 17 Confidence: 9.1% Identity: 18% PDB header:ion transport Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: bacteriorhodopsin k intermediate at 1.43 a resolution Phyre2 PDB 1m0k chain A Region: 296 - 312 Aligned: 17 Modelled: 17 Confidence: 9.1% Identity: 18% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 3qnq chain D Region: 7 - 243 Aligned: 207 Modelled: 211 Confidence: 8.7% Identity: 16% 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 1 c1bctA_ 2 d2r6gf1 3 c2l2tA_ 4 d1z21a1 5 c2i2xO_ 6 d1tm9a_ 7 c3a7kD_ 8 d1e12a_ 9 c2jagA_ 10 c3ddlB_ 11 d1uaza_ 12 d1vkeb_ 13 c3am6C_ 14 d1h2sa_ 15 d2axti1 16 d1xioa_ 17 c1xioA_ 18 c1m0kA_ 19 d1m0ka_ 20 c3qnqD_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 c1bctA_ 47.7 18 PDB header:photoreceptor Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: three-dimensional structure of proteolytic fragment 163-2312 of bacterioopsin determined from nuclear magnetic3 resonance data in solution 2 d2r6gf1 37.0 12 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 3 c2l2tA_ 18.8 24 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 4 d1z21a1 18.2 19 Fold:Type III secretion system domain Superfamily:Type III secretion system domain Family:YopR Core 5 c2i2xO_ 16.9 24 PDB header:transferase Chain: O: PDB Molecule:methyltransferase 1; PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri 6 d1tm9a_ 12.7 32 Fold:Hypothetical protein MG354 Superfamily:Hypothetical protein MG354 Family:Hypothetical protein MG354 7 c3a7kD_ 12.7 25 PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis 8 d1e12a_ 12.2 21 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 9 c2jagA_ 11.8 21 PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v 10 c3ddlB_ 11.1 10 PDB header:transport protein Chain: B: PDB Molecule:xanthorhodopsin; PDBTitle: crystallographic structure of xanthorhodopsin, a light-2 driven ion pump with dual chromophore 11 d1uaza_ 9.9 24 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 12 d1vkeb_ 9.9 19 Fold:AhpD-like Superfamily:AhpD-like Family:CMD-like 13 c3am6C_ 9.6 27 PDB header:transport protein Chain: C: PDB Molecule:rhodopsin-2; PDBTitle: crystal structure of the proton pumping rhodopsin ar2 from marine alga2 acetabularia acetabulum 14 d1h2sa_ 9.5 21 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 15 d2axti1 9.3 26 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein I, PsbI Family:PsbI-like 16 d1xioa_ 9.2 25 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 17 c1xioA_ 9.2 25 PDB header:signaling protein Chain: A: PDB Molecule:anabaena sensory rhodopsin; PDBTitle: anabaena sensory rhodopsin 18 c1m0kA_ 9.1 18 PDB header:ion transport Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: bacteriorhodopsin k intermediate at 1.43 a resolution 19 d1m0ka_ 9.1 18 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 20 c3qnqD_ 8.7 16 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 21 c2qtyB_ not modelled 8.3 24 PDB header:hydrolase Chain: B: PDB Molecule:poly(adp-ribose) glycohydrolase arh3; PDBTitle: crystal structure of mouse adp-ribosylhydrolase 3 (marh3) 22 d1c8sa_ not modelled 8.1 18 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 23 d1xmeb2 not modelled 7.2 36 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 24 c2obuA_ not modelled 7.1 19 PDB header:hormone/growth factor Chain: A: PDB Molecule:gastric inhibitory polypeptide; PDBTitle: solution structure of gip in tfe/water 25 c3dadA_ not modelled 6.5 21 PDB header:signaling protein Chain: A: PDB Molecule:fh1/fh2 domain-containing protein 1; PDBTitle: crystal structure of the n-terminal regulatory domains of2 the formin fhod1 26 d1bl0a2 not modelled 6.1 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 27 c3ia8A_ not modelled 5.8 40 PDB header:metal binding protein Chain: A: PDB Molecule:thap domain-containing protein 4; PDBTitle: the structure of the c-terminal heme nitrobindin domain of thap2 domain-containing protein 4 from homo sapiens 28 c3iz6T_ not modelled 5.4 71 PDB header:ribosome Chain: T: PDB Molecule:40s ribosomal protein s21 (s21e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome

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