Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	R	V	L	H	F	V	L	A	L	A	V	V	A	I	L	A	L	L	V	S	S	D	R	K	K	I	R	I	R	Y	V	I	Q	L	L	V	I	E	V	L	L	A	W	F	F	L	N	S	D	V	G	L	G	F	V	K	G	F
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	E	M	F	E	K	L	L	G	F	A	N	E	G	T	N	F	V	F	G	S	M	N	D	Q	G	L	A	F	F	F	L	K	V	L	C	P	I	V	F	I	S	A	L	I	G	I	L	Q	H	I	R	V	L	P	V	I	I	R	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	G	F	L	L	S	K	V	N	G	M	G	K	L	E	S	F	N	A	V	S	S	L	I	L	G	Q	S	E	N	F	I	A	Y	K	D	I	L	G	K	I	S	R	N	R	M	Y	T	M	A	A	T	A	M	S	T	V	S	M	S
Secondary structure
SS confidence
Disorder											?			?	?	?	?													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	V	G	A	Y	M	T	M	L	E	P	K	Y	V	V	A	A	L	V	L	N	M	F	S	T	F	I	V	L	S	L	I	N	P	Y	R	V	D	A	S	E	E	N	I	Q	M	S	N	L	H	E	G	Q	S	F	F	E	M	L	G
Secondary structure
SS confidence
Disorder												?																											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	Y	I	L	A	G	F	K	V	A	I	I	V	A	A	M	L	I	G	F	I	A	L	I	A	A	L	N	A	L	F	A	T	V	T	G	W	F	G	Y	S	I	S	F	Q	G	I	L	G	Y	I	F	Y	P	I	A	W	V	M	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	P	S	S	E	A	L	Q	V	G	S	I	M	A	T	K	L	V	S	N	E	F	V	A	M	M	D	L	Q	K	I	A	S	T	L	S	P	R	A	E	G	I	I	S	V	F	L	V	S	F	A	N	F	S	S	I	G	I	I	A
Secondary structure
SS confidence
Disorder																																?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400
Sequence		G	A	V	K	G	L	N	E	E	Q	G	N	V	V	S	R	F	G	L	K	L	V	Y	G	S	T	L	V	S	V	L	S	A	S	I	A	A	L	V	L
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 2r6g chain F domain 1 Region: 4 - 53 Aligned: 49 Modelled: 50 Confidence: 51.6% Identity: 20% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 1bct chain A Region: 287 - 302 Aligned: 16 Modelled: 16 Confidence: 41.1% Identity: 25% 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 1tm9 chain A Region: 80 - 114 Aligned: 33 Modelled: 35 Confidence: 22.9% Identity: 27% Fold: Hypothetical protein MG354 Superfamily: Hypothetical protein MG354 Family: Hypothetical protein MG354 Phyre2 PDB 1z21 chain A domain 1 Region: 154 - 169 Aligned: 16 Modelled: 16 Confidence: 18.4% Identity: 6% Fold: Type III secretion system domain Superfamily: Type III secretion system domain Family: YopR Core Phyre2 PDB 2i2x chain O Region: 348 - 385 Aligned: 33 Modelled: 38 Confidence: 18.3% Identity: 15% PDB header:transferase Chain: O: PDB Molecule:methyltransferase 1; PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri Phyre2 PDB 1bl0 chain A Region: 267 - 370 Aligned: 95 Modelled: 104 Confidence: 11.0% Identity: 9% PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex Phyre2 PDB 3ddl chain B Region: 287 - 314 Aligned: 28 Modelled: 28 Confidence: 10.4% Identity: 21% 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 1e12 chain A Region: 287 - 300 Aligned: 14 Modelled: 14 Confidence: 9.0% Identity: 36% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 3oou chain A Region: 266 - 370 Aligned: 89 Modelled: 89 Confidence: 8.8% Identity: 7% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua Phyre2 PDB 2jag chain A Region: 287 - 300 Aligned: 14 Modelled: 14 Confidence: 8.6% Identity: 36% PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v Phyre2 PDB 3cx5 chain D domain 2 Region: 2 - 33 Aligned: 31 Modelled: 32 Confidence: 8.4% Identity: 19% Fold: Single transmembrane helix Superfamily: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Phyre2 PDB 3a7k chain D Region: 287 - 302 Aligned: 16 Modelled: 16 Confidence: 8.3% Identity: 38% PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis Phyre2 PDB 1uaz chain A Region: 287 - 302 Aligned: 16 Modelled: 16 Confidence: 7.6% Identity: 31% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 1xme chain B domain 2 Region: 255 - 265 Aligned: 11 Modelled: 11 Confidence: 7.2% Identity: 82% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2l2t chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 7.1% Identity: 28% 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 1ppj chain D domain 2 Region: 2 - 33 Aligned: 31 Modelled: 32 Confidence: 7.1% Identity: 16% Fold: Single transmembrane helix Superfamily: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Phyre2 PDB 1m0k chain A Region: 287 - 302 Aligned: 16 Modelled: 16 Confidence: 6.9% Identity: 25% PDB header:ion transport Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: bacteriorhodopsin k intermediate at 1.43 a resolution Phyre2 PDB 1m0k chain A Region: 287 - 302 Aligned: 16 Modelled: 16 Confidence: 6.9% Identity: 25% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 3am6 chain C Region: 286 - 300 Aligned: 15 Modelled: 15 Confidence: 6.9% Identity: 33% 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: 287 - 300 Aligned: 14 Modelled: 14 Confidence: 6.8% Identity: 29% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 1 d2r6gf1 2 c1bctA_ 3 d1tm9a_ 4 d1z21a1 5 c2i2xO_ 6 c1bl0A_ 7 c3ddlB_ 8 d1e12a_ 9 c3oouA_ 10 c2jagA_ 11 d3cx5d2 12 c3a7kD_ 13 d1uaza_ 14 d1xmeb2 15 c2l2tA_ 16 d1ppjd2 17 c1m0kA_ 18 d1m0ka_ 19 c3am6C_ 20 d1h2sa_ 21 22 23 24 25 26

Detailed template information

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

1 d2r6gf1 51.6 20 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 2 c1bctA_ 41.1 25 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 3 d1tm9a_ 22.9 27 Fold:Hypothetical protein MG354 Superfamily:Hypothetical protein MG354 Family:Hypothetical protein MG354 4 d1z21a1 18.4 6 Fold:Type III secretion system domain Superfamily:Type III secretion system domain Family:YopR Core 5 c2i2xO_ 18.3 15 PDB header:transferase Chain: O: PDB Molecule:methyltransferase 1; PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri 6 c1bl0A_ 11.0 9 PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex 7 c3ddlB_ 10.4 21 PDB header:transport protein Chain: B: PDB Molecule:xanthorhodopsin; PDBTitle: crystallographic structure of xanthorhodopsin, a light-2 driven ion pump with dual chromophore 8 d1e12a_ 9.0 36 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 9 c3oouA_ 8.8 7 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua 10 c2jagA_ 8.6 36 PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v 11 d3cx5d2 8.4 19 Fold:Single transmembrane helix Superfamily:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor 12 c3a7kD_ 8.3 38 PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis 13 d1uaza_ 7.6 31 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 14 d1xmeb2 7.2 82 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 15 c2l2tA_ 7.1 28 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 16 d1ppjd2 7.1 16 Fold:Single transmembrane helix Superfamily:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor 17 c1m0kA_ 6.9 25 PDB header:ion transport Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: bacteriorhodopsin k intermediate at 1.43 a resolution 18 d1m0ka_ 6.9 25 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 19 c3am6C_ 6.9 33 PDB header:transport protein Chain: C: PDB Molecule:rhodopsin-2; PDBTitle: crystal structure of the proton pumping rhodopsin ar2 from marine alga2 acetabularia acetabulum 20 d1h2sa_ 6.8 29 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 21 c3iz6T_ not modelled 6.7 19 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 22 c3dadA_ not modelled 6.4 18 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 23 c2obuA_ not modelled 6.4 19 PDB header:hormone/growth factor Chain: A: PDB Molecule:gastric inhibitory polypeptide; PDBTitle: solution structure of gip in tfe/water 24 c1xioA_ not modelled 6.1 38 PDB header:signaling protein Chain: A: PDB Molecule:anabaena sensory rhodopsin; PDBTitle: anabaena sensory rhodopsin 25 d1xioa_ not modelled 6.1 38 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 26 d1c8sa_ not modelled 5.9 25 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-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

---

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