Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	W	S	L	T	Q	N	K	L	L	A	F	H	R	L	M	R	T	D	K	P	I	G	A	L	L	L	L	W	P	T	L	W	A	L	W	V	A	T	P	G	V	P	Q	L	W	I	L	A	V	F	V	A	G	V	W	L	M	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	A	G	C	V	V	N	D	Y	A	D	R	K	F	D	G	H	V	K	R	T	A	N	R	P	L	P	S	G	A	V	T	E	K	E	A	R	A	L	F	V	V	L	V	L	I	S	F	L	L	V	L	T	L	N	T	M	T	I	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	S	I	A	A	L	A	L	A	W	V	Y	P	F	M	K	R	Y	T	H	L	P	Q	V	V	L	G	A	A	F	G	W	S	I	P	M	A	F	A	A	V	S	E	S	V	P	L	S	C	W	L	M	F	L	A	N	I	L	W	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	A	Y	D	T	Q	Y	A	M	V	D	R	D	D	D	V	K	I	G	I	K	S	T	A	I	L	F	G	Q	Y	D	K	L	I	I	G	I	L	Q	I	G	V	L	A	L	M	A	I	I	G	E	L	N	G	L	G	W	G	Y	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290
Sequence		W	S	I	L	V	A	G	A	L	F	V	Y	Q	Q	K	L	I	A	N	R	E	R	E	A	C	F	K	A	F	M	N	N	N	Y	V	G	L	V	L	F	L	G	L	A	M	S	Y	W	H	F
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 3ts7 chain B Region: 32 - 213 Aligned: 179 Modelled: 182 Confidence: 96.0% Identity: 16% PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of farnesyl diphosphate synthase (target efi-501951)2 from methylococcus capsulatus Phyre2 PDB 3m9u chain D Region: 32 - 216 Aligned: 181 Modelled: 182 Confidence: 91.2% Identity: 10% PDB header:transferase Chain: D: PDB Molecule:farnesyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from lactobacillus brevis atcc 367 Phyre2 PDB 3lsn chain A Region: 32 - 213 Aligned: 178 Modelled: 179 Confidence: 79.5% 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 1rqj chain A Region: 32 - 213 Aligned: 179 Modelled: 179 Confidence: 72.6% Identity: 12% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 1v4e chain A Region: 31 - 208 Aligned: 169 Modelled: 178 Confidence: 52.4% Identity: 17% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 3oyr chain B Region: 32 - 207 Aligned: 170 Modelled: 176 Confidence: 49.2% Identity: 14% 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 3dh4 chain A Region: 46 - 228 Aligned: 174 Modelled: 176 Confidence: 42.1% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus Phyre2 PDB 3npk chain B Region: 149 - 227 Aligned: 79 Modelled: 79 Confidence: 41.9% Identity: 9% PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: the crystal structure of geranyltranstransferase from campylobacter2 jejuni Phyre2 PDB 3p8l chain B Region: 149 - 227 Aligned: 79 Modelled: 79 Confidence: 41.0% Identity: 11% PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of polyprenyl synthase from enterococcus faecalis2 v583 Phyre2 PDB 3aqb chain D Region: 32 - 207 Aligned: 170 Modelled: 176 Confidence: 40.5% Identity: 14% 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 2j1o chain A Region: 148 - 216 Aligned: 66 Modelled: 69 Confidence: 40.1% Identity: 8% PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba Phyre2 PDB 3llw chain A Region: 45 - 213 Aligned: 162 Modelled: 166 Confidence: 38.3% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase (ispa); PDBTitle: crystal structure of geranyltransferase from helicobacter2 pylori 26695 Phyre2 PDB 3mzv chain B Region: 32 - 207 Aligned: 171 Modelled: 176 Confidence: 30.3% Identity: 15% PDB header:transferase Chain: B: PDB Molecule:decaprenyl diphosphate synthase; PDBTitle: crystal structure of a decaprenyl diphosphate synthase from2 rhodobacter capsulatus Phyre2 PDB 2j1p chain B Region: 32 - 213 Aligned: 176 Modelled: 179 Confidence: 28.8% Identity: 11% PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba in2 complex with ggpp Phyre2 PDB 3kra chain B Region: 153 - 227 Aligned: 75 Modelled: 75 Confidence: 25.8% Identity: 11% PDB header:transferase Chain: B: PDB Molecule:geranyl diphosphate synthase small subunit; PDBTitle: mint heterotetrameric geranyl pyrophosphate synthase in2 complex with magnesium Phyre2 PDB 2e8x chain B Region: 153 - 227 Aligned: 74 Modelled: 75 Confidence: 21.1% Identity: 8% PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: s. cerevisiae geranylgeranyl pyrophosphate synthase in2 complex with magnesium and gpp Phyre2 PDB 1dih chain A domain 2 Region: 52 - 85 Aligned: 34 Modelled: 34 Confidence: 18.0% Identity: 24% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Dihydrodipicolinate reductase-like Phyre2 PDB 1wmw chain A Region: 32 - 207 Aligned: 169 Modelled: 176 Confidence: 17.5% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl diphosphate synthetase; PDBTitle: crystal structure of geranulgeranyl diphosphate synthase from thermus2 thermophilus Phyre2 PDB 1wy0 chain A Region: 32 - 207 Aligned: 171 Modelled: 176 Confidence: 13.7% Identity: 12% PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthetase from2 pyrococcus horikoshii ot3 Phyre2 PDB 3ez3 chain A Region: 149 - 229 Aligned: 80 Modelled: 81 Confidence: 13.6% Identity: 9% 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 1 c3ts7B_ 2 c3m9uD_ 3 c3lsnA_ 4 d1rqja_ 5 d1v4ea_ 6 c3oyrB_ 7 c3dh4A_ 8 c3npkB_ 9 c3p8lB_ 10 c3aqbD_ 11 c2j1oA_ 12 c3llwA_ 13 c3mzvB_ 14 c2j1pB_ 15 c3kraB_ 16 c2e8xB_ 17 d1diha2 18 c1wmwA_ 19 c1wy0A_ 20 c3ez3A_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 c3ts7B_ 96.0 16 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of farnesyl diphosphate synthase (target efi-501951)2 from methylococcus capsulatus 2 c3m9uD_ 91.2 10 PDB header:transferase Chain: D: PDB Molecule:farnesyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from lactobacillus brevis atcc 367 3 c3lsnA_ 79.5 16 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of putative geranyltranstransferase from pseudomonas2 fluorescens pf-5 complexed with magnesium 4 d1rqja_ 72.6 12 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 5 d1v4ea_ 52.4 17 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 6 c3oyrB_ 49.2 14 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 7 c3dh4A_ 42.1 16 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 8 c3npkB_ 41.9 9 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: the crystal structure of geranyltranstransferase from campylobacter2 jejuni 9 c3p8lB_ 41.0 11 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of polyprenyl synthase from enterococcus faecalis2 v583 10 c3aqbD_ 40.5 14 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 11 c2j1oA_ 40.1 8 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba 12 c3llwA_ 38.3 14 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase (ispa); PDBTitle: crystal structure of geranyltransferase from helicobacter2 pylori 26695 13 c3mzvB_ 30.3 15 PDB header:transferase Chain: B: PDB Molecule:decaprenyl diphosphate synthase; PDBTitle: crystal structure of a decaprenyl diphosphate synthase from2 rhodobacter capsulatus 14 c2j1pB_ 28.8 11 PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba in2 complex with ggpp 15 c3kraB_ 25.8 11 PDB header:transferase Chain: B: PDB Molecule:geranyl diphosphate synthase small subunit; PDBTitle: mint heterotetrameric geranyl pyrophosphate synthase in2 complex with magnesium 16 c2e8xB_ 21.1 8 PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: s. cerevisiae geranylgeranyl pyrophosphate synthase in2 complex with magnesium and gpp 17 d1diha2 18.0 24 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 18 c1wmwA_ 17.5 13 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl diphosphate synthetase; PDBTitle: crystal structure of geranulgeranyl diphosphate synthase from thermus2 thermophilus 19 c1wy0A_ 13.7 12 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthetase from2 pyrococcus horikoshii ot3 20 c3ez3A_ 13.6 9 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 21 c2ftzA_ not modelled 12.7 12 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 22 c3nf2A_ not modelled 12.4 13 PDB header:transferase Chain: A: PDB Molecule:putative polyprenyl synthetase; PDBTitle: crystal structure of polyprenyl synthetase from streptomyces2 coelicolor a3(2) 23 d2q80a1 not modelled 7.5 14 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 24 d1vm6a2 not modelled 6.0 15 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 25 c2xq2A_ not modelled 5.5 15 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 26 c3lomA_ not modelled 5.4 16 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of geranyltransferase from legionella2 pneumophila 27 c3sahA_ not modelled 5.3 17 PDB header:hydrolase Chain: A: PDB Molecule:exosome component 10; PDBTitle: crystal structure of the human rrp6 catalytic domain with y436a2 mutation in the catalytic site 28 c1drwA_ not modelled 5.2 24 PDB header:oxidoreductase Chain: A: PDB Molecule:dihydrodipicolinate reductase; PDBTitle: escherichia coli dhpr/nhdh complex 29 c3tc1A_ not modelled 5.2 10 PDB header:transferase Chain: A: PDB Molecule:octaprenyl pyrophosphate synthase; PDBTitle: crystal structure of octaprenyl pyrophosphate synthase from2 helicobacter pylori 30 c3rmgB_ not modelled 5.1 15 PDB header:transferase Chain: B: PDB Molecule:octaprenyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase from2 bacteroides thetaiotaomicron

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