Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	E	Q	Q	I	S	R	T	Q	A	W	L	E	S	L	R	P	K	T	L	P	L	A	F	A	A	I	I	V	G	T	A	L	A	W	W	Q	G	H	F	D	P	L	V	A	L	L	A	L	I	T	A	G	L	L	Q	I	L	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	L	A	N	D	Y	G	D	A	V	K	G	S	D	K	P	D	R	I	G	P	L	R	G	M	Q	K	G	V	I	T	Q	Q	E	M	K	R	A	L	I	I	T	V	V	L	I	C	L	S	G	L	A	L	V	A	V	A	C	H	T
Secondary structure
SS confidence
Disorder																						?		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	A	D	F	V	G	F	L	I	L	G	G	L	S	I	I	A	A	I	T	Y	T	V	G	N	R	P	Y	G	Y	I	G	L	G	D	I	S	V	L	V	F	F	G	W	L	S	V	M	G	S	W	Y	L	Q	A	H	T	L	I	P
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	L	I	L	P	A	T	A	C	G	L	L	A	T	A	V	L	N	I	N	N	L	R	D	I	N	S	D	R	E	N	G	K	N	T	L	V	V	R	L	G	E	V	N	A	R	R	Y	H	A	C	L	L	M	G	S	L	V	C	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		A	L	F	N	L	F	S	L	H	S	L	W	G	W	L	F	L	L	A	A	P	L	L	V	K	Q	A	R	Y	V	M	R	E	M	D	P	V	A	M	R	P	M	L	E	R	T	V	K	G	A	L	L	T	N	L	L	F	V	L	G
Secondary structure
SS confidence
Disorder																																	?		?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		I	F	L	S	Q	W	A	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 3m9u chain D Region: 27 - 240 Aligned: 207 Modelled: 212 Confidence: 94.1% Identity: 14% PDB header:transferase Chain: D: PDB Molecule:farnesyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from lactobacillus brevis atcc 367 Phyre2 PDB 3ts7 chain B Region: 27 - 233 Aligned: 200 Modelled: 207 Confidence: 92.1% Identity: 11% PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of farnesyl diphosphate synthase (target efi-501951)2 from methylococcus capsulatus Phyre2 PDB 3kra chain B Region: 162 - 241 Aligned: 79 Modelled: 80 Confidence: 66.9% Identity: 14% PDB header:transferase Chain: B: PDB Molecule:geranyl diphosphate synthase small subunit; PDBTitle: mint heterotetrameric geranyl pyrophosphate synthase in2 complex with magnesium Phyre2 PDB 3oyr chain B Region: 32 - 224 Aligned: 184 Modelled: 186 Confidence: 62.2% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:trans-isoprenyl diphosphate synthase; PDBTitle: crystal structure of polyprenyl synthase from caulobacter crescentus2 cb15 complexed with calcium and isoprenyl diphosphate Phyre2 PDB 3mzv chain B Region: 32 - 220 Aligned: 180 Modelled: 182 Confidence: 56.8% Identity: 12% PDB header:transferase Chain: B: PDB Molecule:decaprenyl diphosphate synthase; PDBTitle: crystal structure of a decaprenyl diphosphate synthase from2 rhodobacter capsulatus Phyre2 PDB 3lsn chain A Region: 32 - 237 Aligned: 200 Modelled: 206 Confidence: 54.2% 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 3ipi chain A Region: 162 - 240 Aligned: 77 Modelled: 79 Confidence: 53.0% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of a geranyltranstransferase from the2 methanosarcina mazei Phyre2 PDB 3aqb chain D Region: 32 - 225 Aligned: 185 Modelled: 187 Confidence: 42.4% Identity: 12% PDB header:transferase Chain: D: PDB Molecule:component b of hexaprenyl diphosphate synthase; PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium Phyre2 PDB 1v4e chain A Region: 29 - 224 Aligned: 183 Modelled: 196 Confidence: 37.7% Identity: 12% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 2ftz chain A Region: 162 - 240 Aligned: 77 Modelled: 79 Confidence: 36.2% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of geranyltranstransferase (ec 2.5.1.10) (tm0161)2 from thermotoga maritima at 1.90 a resolution Phyre2 PDB 2q80 chain A domain 1 Region: 162 - 304 Aligned: 141 Modelled: 143 Confidence: 35.0% Identity: 13% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 2e8x chain B Region: 162 - 240 Aligned: 77 Modelled: 79 Confidence: 34.1% Identity: 14% PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: s. cerevisiae geranylgeranyl pyrophosphate synthase in2 complex with magnesium and gpp Phyre2 PDB 2j1o chain A Region: 164 - 237 Aligned: 71 Modelled: 74 Confidence: 31.2% Identity: 8% PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba Phyre2 PDB 1wy0 chain A Region: 32 - 224 Aligned: 184 Modelled: 186 Confidence: 27.0% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthetase from2 pyrococcus horikoshii ot3 Phyre2 PDB 1rqj chain A Region: 32 - 229 Aligned: 193 Modelled: 198 Confidence: 23.7% Identity: 12% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 3ez3 chain A Region: 162 - 242 Aligned: 80 Modelled: 81 Confidence: 22.0% Identity: 11% 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 3m0g chain B Region: 162 - 237 Aligned: 75 Modelled: 76 Confidence: 21.4% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:farnesyl diphosphate synthase; PDBTitle: crystal structure of putative farnesyl diphosphate synthase from2 rhodobacter capsulatus Phyre2 PDB 3nf2 chain A Region: 32 - 220 Aligned: 180 Modelled: 182 Confidence: 19.8% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:putative polyprenyl synthetase; PDBTitle: crystal structure of polyprenyl synthetase from streptomyces2 coelicolor a3(2) Phyre2 PDB 3npk chain B Region: 162 - 304 Aligned: 143 Modelled: 143 Confidence: 19.2% Identity: 17% PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: the crystal structure of geranyltranstransferase from campylobacter2 jejuni Phyre2 PDB 2h8o chain A Region: 162 - 241 Aligned: 79 Modelled: 80 Confidence: 18.1% Identity: 20% PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: the 1.6a crystal structure of the geranyltransferase from2 agrobacterium tumefaciens Phyre2 1 c3m9uD_ 2 c3ts7B_ 3 c3kraB_ 4 c3oyrB_ 5 c3mzvB_ 6 c3lsnA_ 7 c3ipiA_ 8 c3aqbD_ 9 d1v4ea_ 10 c2ftzA_ 11 d2q80a1 12 c2e8xB_ 13 c2j1oA_ 14 c1wy0A_ 15 d1rqja_ 16 c3ez3A_ 17 c3m0gB_ 18 c3nf2A_ 19 c3npkB_ 20 c2h8oA_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 c3m9uD_ 94.1 14 PDB header:transferase Chain: D: PDB Molecule:farnesyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from lactobacillus brevis atcc 367 2 c3ts7B_ 92.1 11 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of farnesyl diphosphate synthase (target efi-501951)2 from methylococcus capsulatus 3 c3kraB_ 66.9 14 PDB header:transferase Chain: B: PDB Molecule:geranyl diphosphate synthase small subunit; PDBTitle: mint heterotetrameric geranyl pyrophosphate synthase in2 complex with magnesium 4 c3oyrB_ 62.2 13 PDB header:transferase Chain: B: PDB Molecule:trans-isoprenyl diphosphate synthase; PDBTitle: crystal structure of polyprenyl synthase from caulobacter crescentus2 cb15 complexed with calcium and isoprenyl diphosphate 5 c3mzvB_ 56.8 12 PDB header:transferase Chain: B: PDB Molecule:decaprenyl diphosphate synthase; PDBTitle: crystal structure of a decaprenyl diphosphate synthase from2 rhodobacter capsulatus 6 c3lsnA_ 54.2 16 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of putative geranyltranstransferase from pseudomonas2 fluorescens pf-5 complexed with magnesium 7 c3ipiA_ 53.0 13 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of a geranyltranstransferase from the2 methanosarcina mazei 8 c3aqbD_ 42.4 12 PDB header:transferase Chain: D: PDB Molecule:component b of hexaprenyl diphosphate synthase; PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium 9 d1v4ea_ 37.7 12 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 10 c2ftzA_ 36.2 19 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of geranyltranstransferase (ec 2.5.1.10) (tm0161)2 from thermotoga maritima at 1.90 a resolution 11 d2q80a1 35.0 13 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 12 c2e8xB_ 34.1 14 PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: s. cerevisiae geranylgeranyl pyrophosphate synthase in2 complex with magnesium and gpp 13 c2j1oA_ 31.2 8 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba 14 c1wy0A_ 27.0 13 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthetase from2 pyrococcus horikoshii ot3 15 d1rqja_ 23.7 12 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 16 c3ez3A_ 22.0 11 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 17 c3m0gB_ 21.4 13 PDB header:transferase Chain: B: PDB Molecule:farnesyl diphosphate synthase; PDBTitle: crystal structure of putative farnesyl diphosphate synthase from2 rhodobacter capsulatus 18 c3nf2A_ 19.8 15 PDB header:transferase Chain: A: PDB Molecule:putative polyprenyl synthetase; PDBTitle: crystal structure of polyprenyl synthetase from streptomyces2 coelicolor a3(2) 19 c3npkB_ 19.2 17 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: the crystal structure of geranyltranstransferase from campylobacter2 jejuni 20 c2h8oA_ 18.1 20 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: the 1.6a crystal structure of the geranyltransferase from2 agrobacterium tumefaciens 21 c2o1oB_ not modelled 15.6 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative farnesyl pyrophosphate synthase; PDBTitle: cryptosporidium parvum putative polyprenyl pyrophosphate2 synthase (cgd4_2550) in complex with risedronate. 22 c1wmwA_ not modelled 14.7 15 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl diphosphate synthetase; PDBTitle: crystal structure of geranulgeranyl diphosphate synthase from thermus2 thermophilus 23 c3p8lB_ not modelled 14.5 20 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of polyprenyl synthase from enterococcus faecalis2 v583 24 c3llwA_ not modelled 13.9 9 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase (ispa); PDBTitle: crystal structure of geranyltransferase from helicobacter2 pylori 26695 25 c2forB_ not modelled 13.7 22 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of the shigella flexneri farnesyl pyrophosphate2 synthase complex with an isopentenyl pyrophosphate 26 c2f94F_ not modelled 11.3 12 PDB header:transferase Chain: F: PDB Molecule:farnesyl diphosphate synthase; PDBTitle: crystal structure of human fpps in complex with ibandronate 27 c1yhlA_ not modelled 9.7 9 PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase; PDBTitle: structure of the complex of trypanosoma cruzi farnesyl diphosphate2 synthase with risedronate, dmapp and mg+2 28 c3dh4A_ not modelled 8.7 6 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 29 c3cp6A_ not modelled 7.2 11 PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthetase; PDBTitle: crystal structure of human farnesyl diphosphate synthase (t201a2 mutant) complexed with mg and biphosphonate inhibitor 30 d1q90b_ not modelled 6.5 8 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 31 d1diha2 not modelled 5.4 17 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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