Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	L	S	R	T	Q	I	V	N	W	L	T	R	C	G	D	I	F	S	T	E	S	E	Y	L	T	G	L	D	R	E	I	G	D	A	D	H	G	L	N	M	N	R	G	F	S	K	V	V	E	K	L	P	A	I	A	D	K	D
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	G	F	I	L	K	N	T	G	M	T	L	L	S	S	V	G	G	A	S	G	P	L	F	G	T	F	F	I	R	A	A	Q	A	T	Q	A	R	Q	S	L	T	L	E	E	L	Y	Q	M	F	R	D	G	A	D	G	V	I	S	R
Secondary structure
SS confidence
Disorder																?	?		?																	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	K	A	E	P	G	D	K	T	M	C	D	V	W	V	P	V	V	E	S	L	R	Q	S	S	E	Q	N	L	S	V	P	V	A	L	E	A	A	S	S	I	A	E	S	A	A	Q	S	T	I	T	M	Q	A	R	K	G	R	A	S
Secondary structure
SS confidence
Disorder																										?	?	?																									?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210
Sequence		Y	L	G	E	R	S	I	G	H	Q	D	P	G	A	T	S	V	M	F	M	M	Q	M	L	A	L	A	A	K	E
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 2btd chain A Region: 2 - 210 Aligned: 209 Modelled: 209 Confidence: 100.0% Identity: 100% PDB header:transferase Chain: A: PDB Molecule:pts-dependent dihydroxyacetone kinase; PDBTitle: crystal structure of dhal from e. coli Phyre2 PDB 3cr3 chain A domain 1 Region: 3 - 208 Aligned: 190 Modelled: 206 Confidence: 100.0% Identity: 35% Fold: DhaL-like Superfamily: DhaL-like Family: DhaL-like Phyre2 PDB 1un8 chain A domain 1 Region: 4 - 207 Aligned: 186 Modelled: 199 Confidence: 100.0% Identity: 25% Fold: DhaL-like Superfamily: DhaL-like Family: DhaL-like Phyre2 PDB 1un9 chain B Region: 4 - 207 Aligned: 181 Modelled: 199 Confidence: 100.0% Identity: 26% PDB header:kinase Chain: B: PDB Molecule:dihydroxyacetone kinase; PDBTitle: crystal structure of the dihydroxyacetone kinase from c.2 freundii in complex with amp-pnp and mg2+ Phyre2 PDB 2r6g chain F domain 1 Region: 16 - 37 Aligned: 22 Modelled: 22 Confidence: 40.0% Identity: 9% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 1a6d chain B domain 1 Region: 23 - 125 Aligned: 103 Modelled: 103 Confidence: 33.1% Identity: 17% Fold: GroEL equatorial domain-like Superfamily: GroEL equatorial domain-like Family: Group II chaperonin (CCT, TRIC), ATPase domain Phyre2 PDB 2hh6 chain A domain 1 Region: 103 - 155 Aligned: 53 Modelled: 53 Confidence: 21.4% Identity: 8% Fold: Left-handed superhelix Superfamily: BH3980-like Family: BH3980-like Phyre2 PDB 1f61 chain A Region: 3 - 52 Aligned: 50 Modelled: 50 Confidence: 21.1% Identity: 14% Fold: TIM beta/alpha-barrel Superfamily: Phosphoenolpyruvate/pyruvate domain Family: Phosphoenolpyruvate mutase/Isocitrate lyase-like Phyre2 PDB 2ax3 chain A domain 2 Region: 8 - 39 Aligned: 32 Modelled: 32 Confidence: 14.0% Identity: 16% Fold: YjeF N-terminal domain-like Superfamily: YjeF N-terminal domain-like Family: YjeF N-terminal domain-like Phyre2 PDB 2dg2 chain D Region: 11 - 39 Aligned: 29 Modelled: 29 Confidence: 12.6% Identity: 17% PDB header:protein binding Chain: D: PDB Molecule:apolipoprotein a-i binding protein; PDBTitle: crystal structure of mouse apolipoprotein a-i binding2 protein Phyre2 PDB 2lch chain A Region: 1 - 120 Aligned: 100 Modelled: 100 Confidence: 11.2% Identity: 9% PDB header:de novo protein Chain: A: PDB Molecule:protein or38; PDBTitle: solution nmr structure of a protein with a redesigned hydrophobic2 core, northeast structural genomics consortium target or38 Phyre2 PDB 1rvg chain A Region: 88 - 179 Aligned: 85 Modelled: 92 Confidence: 10.2% Identity: 11% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: Class II FBP aldolase Phyre2 PDB 2r5r chain A Region: 39 - 68 Aligned: 30 Modelled: 29 Confidence: 9.4% Identity: 17% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0343 protein ne1163; PDBTitle: the crystal structure of duf198 from nitrosomonas europaea2 atcc 19718 Phyre2 PDB 2g3q chain A domain 1 Region: 1 - 26 Aligned: 26 Modelled: 26 Confidence: 9.3% Identity: 19% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 3d3k chain D Region: 2 - 39 Aligned: 38 Modelled: 38 Confidence: 9.2% Identity: 11% PDB header:protein binding Chain: D: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of human edc3p Phyre2 PDB 1ify chain A Region: 1 - 26 Aligned: 26 Modelled: 26 Confidence: 8.4% Identity: 27% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 2ax3 chain A Region: 8 - 39 Aligned: 32 Modelled: 32 Confidence: 7.9% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:hypothetical protein tm0922; PDBTitle: crystal structure of a putative carbohydrate kinase (tm0922) from2 thermotoga maritima msb8 at 2.25 a resolution Phyre2 PDB 2cho chain A domain 1 Region: 88 - 156 Aligned: 68 Modelled: 69 Confidence: 7.6% Identity: 16% Fold: Hyaluronidase domain-like Superfamily: Hyaluronidase post-catalytic domain-like Family: Hyaluronidase post-catalytic domain-like Phyre2 PDB 2kdd chain B Region: 29 - 38 Aligned: 10 Modelled: 10 Confidence: 7.0% Identity: 20% PDB header:cell cycle Chain: B: PDB Molecule:borealin; PDBTitle: solution structure of the conserved c-terminal dimerization2 domain of borealin Phyre2 PDB 1q3q chain A domain 1 Region: 23 - 125 Aligned: 103 Modelled: 103 Confidence: 7.0% Identity: 16% Fold: GroEL equatorial domain-like Superfamily: GroEL equatorial domain-like Family: Group II chaperonin (CCT, TRIC), ATPase domain Phyre2 1 c2btdA_ 2 d3cr3a1 3 d1un8a1 4 c1un9B_ 5 d2r6gf1 6 d1a6db1 7 d2hh6a1 8 d1f61a_ 9 d2ax3a2 10 c2dg2D_ 11 c2lchA_ 12 d1rvga_ 13 c2r5rA_ 14 d2g3qa1 15 c3d3kD_ 16 d1ifya_ 17 c2ax3A_ 18 d2choa1 19 c2kddB_ 20 d1q3qa1 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 c2btdA_ 100.0 100 PDB header:transferase Chain: A: PDB Molecule:pts-dependent dihydroxyacetone kinase; PDBTitle: crystal structure of dhal from e. coli 2 d3cr3a1 100.0 35 Fold:DhaL-like Superfamily:DhaL-like Family:DhaL-like 3 d1un8a1 100.0 25 Fold:DhaL-like Superfamily:DhaL-like Family:DhaL-like 4 c1un9B_ 100.0 26 PDB header:kinase Chain: B: PDB Molecule:dihydroxyacetone kinase; PDBTitle: crystal structure of the dihydroxyacetone kinase from c.2 freundii in complex with amp-pnp and mg2+ 5 d2r6gf1 40.0 9 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 6 d1a6db1 33.1 17 Fold:GroEL equatorial domain-like Superfamily:GroEL equatorial domain-like Family:Group II chaperonin (CCT, TRIC), ATPase domain 7 d2hh6a1 21.4 8 Fold:Left-handed superhelix Superfamily:BH3980-like Family:BH3980-like 8 d1f61a_ 21.1 14 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like 9 d2ax3a2 14.0 16 Fold:YjeF N-terminal domain-like Superfamily:YjeF N-terminal domain-like Family:YjeF N-terminal domain-like 10 c2dg2D_ 12.6 17 PDB header:protein binding Chain: D: PDB Molecule:apolipoprotein a-i binding protein; PDBTitle: crystal structure of mouse apolipoprotein a-i binding2 protein 11 c2lchA_ 11.2 9 PDB header:de novo protein Chain: A: PDB Molecule:protein or38; PDBTitle: solution nmr structure of a protein with a redesigned hydrophobic2 core, northeast structural genomics consortium target or38 12 d1rvga_ 10.2 11 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class II FBP aldolase 13 c2r5rA_ 9.4 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0343 protein ne1163; PDBTitle: the crystal structure of duf198 from nitrosomonas europaea2 atcc 19718 14 d2g3qa1 9.3 19 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 15 c3d3kD_ 9.2 11 PDB header:protein binding Chain: D: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of human edc3p 16 d1ifya_ 8.4 27 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 17 c2ax3A_ 7.9 16 PDB header:transferase Chain: A: PDB Molecule:hypothetical protein tm0922; PDBTitle: crystal structure of a putative carbohydrate kinase (tm0922) from2 thermotoga maritima msb8 at 2.25 a resolution 18 d2choa1 7.6 16 Fold:Hyaluronidase domain-like Superfamily:Hyaluronidase post-catalytic domain-like Family:Hyaluronidase post-catalytic domain-like 19 c2kddB_ 7.0 20 PDB header:cell cycle Chain: B: PDB Molecule:borealin; PDBTitle: solution structure of the conserved c-terminal dimerization2 domain of borealin 20 d1q3qa1 7.0 16 Fold:GroEL equatorial domain-like Superfamily:GroEL equatorial domain-like Family:Group II chaperonin (CCT, TRIC), ATPase domain 21 c3d3jA_ not modelled 6.8 11 PDB header:protein binding Chain: A: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of human edc3p 22 d1wgwa_ not modelled 6.6 16 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 23 d1asha_ not modelled 6.5 6 Fold:Globin-like Superfamily:Globin-like Family:Globins 24 d1xo3a_ not modelled 6.3 40 Fold:beta-Grasp (ubiquitin-like) Superfamily:MoaD/ThiS Family:C9orf74 homolog 25 d1x6aa2 not modelled 6.1 50 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 26 d2o3la1 not modelled 6.0 6 Fold:Left-handed superhelix Superfamily:BH3980-like Family:BH3980-like 27 d1x62a1 not modelled 5.9 43 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 28 d1igwa_ not modelled 5.7 20 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like 29 c3d2oB_ not modelled 5.6 10 PDB header:hydrolase, biosynthetic protein Chain: B: PDB Molecule:upf0343 protein ngo0387; PDBTitle: crystal structure of manganese-metallated gtp cyclohydrolase2 type ib 30 c1p58C_ not modelled 5.6 22 PDB header:virus Chain: C: PDB Molecule:major envelope protein e; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 31 d1oqya1 not modelled 5.5 27 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 32 c3pm6B_ not modelled 5.3 19 PDB header:lyase Chain: B: PDB Molecule:putative fructose-bisphosphate aldolase; PDBTitle: crystal structure of a putative fructose-1,6-biphosphate aldolase from2 coccidioides immitis solved by combined sad mr

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