Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	V	W	L	A	E	H	L	V	K	Y	Y	S	G	F	N	V	F	S	Y	L	T	F	R	A	I	V	S	L	L	T	A	L	F	I	S	L	W	M	G	P	R	M	I	A	H	L	Q	K	L	S	F	G	Q	V	V	R	N	D
Secondary structure
SS confidence
Disorder		?																																																					?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	P	E	S	H	F	S	K	R	G	T	P	T	M	G	G	I	M	I	L	T	A	I	V	I	S	V	L	L	W	A	Y	P	S	N	P	Y	V	W	C	V	L	V	V	L	V	G	Y	G	V	I	G	F	V	D	D	Y	R	K	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	R	K	D	T	K	G	L	I	A	R	W	K	Y	F	W	M	S	V	I	A	L	G	V	A	F	A	L	Y	L	A	G	K	D	T	P	A	T	Q	L	V	V	P	F	F	K	D	V	M	P	Q	L	G	L	F	Y	I	L	L	A
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?																										?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		Y	F	V	I	V	G	T	G	N	A	V	N	L	T	D	G	L	D	G	L	A	I	M	P	T	V	F	V	A	G	G	F	A	L	V	A	W	A	T	G	N	M	N	F	A	S	Y	L	H	I	P	Y	L	R	H	A	G	E	L	V
Secondary structure
SS confidence
Disorder																																																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	V	C	T	A	I	V	G	A	G	L	G	F	L	W	F	N	T	Y	P	A	Q	V	F	M	G	D	V	G	S	L	A	L	G	G	A	L	G	I	I	A	V	L	L	R	Q	E	F	L	L	V	I	M	G	G	V	F	V	V	E
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		T	L	S	V	I	L	Q	V	G	S	F	K	L	R	G	Q	R	I	F	R	M	A	P	I	H	H	H	Y	E	L	K	G	W	P	E	P	R	V	I	V	R	F	W	I	I	S	L	M	L	V	L	I	G	L	A	T	L	K	V	R
Secondary structure
SS confidence
Disorder																			?																																							?	?	?	?
Disorder confidence
Sequence
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 3quv chain B Region: 44 - 76 Aligned: 33 Modelled: 33 Confidence: 12.8% Identity: 24% PDB header:transferase Chain: B: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: crystal structure of a trna-guanine-n1-methyltransferase from2 mycobacterium abscessus Phyre2 PDB 3dl8 chain H Region: 7 - 119 Aligned: 113 Modelled: 113 Confidence: 12.5% Identity: 12% PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 2jxp chain A Region: 300 - 328 Aligned: 29 Modelled: 29 Confidence: 11.8% Identity: 14% PDB header:lipoprotein Chain: A: PDB Molecule:putative lipoprotein b; PDBTitle: solution nmr structure of uncharacterized lipoprotein b2 from nitrosomonas europaea. northeast structural genomics3 target ner45a Phyre2 PDB 1p9p chain A Region: 44 - 76 Aligned: 33 Modelled: 33 Confidence: 11.3% Identity: 18% Fold: alpha/beta knot Superfamily: alpha/beta knot Family: tRNA(m1G37)-methyltransferase TrmD Phyre2 PDB 1ual chain A Region: 44 - 76 Aligned: 33 Modelled: 33 Confidence: 10.7% Identity: 21% Fold: alpha/beta knot Superfamily: alpha/beta knot Family: tRNA(m1G37)-methyltransferase TrmD Phyre2 PDB 2aki chain Y Region: 8 - 119 Aligned: 109 Modelled: 109 Confidence: 10.6% Identity: 13% PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli Phyre2 PDB 1o5h chain A Region: 52 - 89 Aligned: 38 Modelled: 38 Confidence: 10.3% Identity: 11% Fold: Methenyltetrahydrofolate cyclohydrolase-like Superfamily: Methenyltetrahydrofolate cyclohydrolase-like Family: Methenyltetrahydrofolate cyclohydrolase-like Phyre2 PDB 3din chain F Region: 8 - 119 Aligned: 112 Modelled: 112 Confidence: 10.1% Identity: 14% PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 3knu chain D Region: 44 - 76 Aligned: 32 Modelled: 33 Confidence: 7.5% Identity: 25% PDB header:transferase Chain: D: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: crystal structure of trna (guanine-n1)-methyltransferase from2 anaplasma phagocytophilum Phyre2 PDB 2c42 chain A domain 2 Region: 263 - 275 Aligned: 13 Modelled: 13 Confidence: 7.5% Identity: 31% Fold: Thiamin diphosphate-binding fold (THDP-binding) Superfamily: Thiamin diphosphate-binding fold (THDP-binding) Family: PFOR PP module Phyre2 PDB 2zqp chain Y Region: 6 - 119 Aligned: 112 Modelled: 114 Confidence: 7.3% Identity: 13% PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: crystal structure of secye translocon from thermus2 thermophilus Phyre2 PDB 3ky7 chain A Region: 44 - 76 Aligned: 32 Modelled: 33 Confidence: 6.8% Identity: 25% PDB header:transferase Chain: A: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: 2.35 angstrom resolution crystal structure of a putative trna2 (guanine-7-)-methyltransferase (trmd) from staphylococcus aureus3 subsp. aureus mrsa252 Phyre2 PDB 3j01 chain A Region: 8 - 119 Aligned: 112 Modelled: 112 Confidence: 6.0% Identity: 13% PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment Phyre2 PDB 2vzn chain A Region: 315 - 328 Aligned: 14 Modelled: 14 Confidence: 5.9% Identity: 36% PDB header:allergen Chain: A: PDB Molecule:venom allergen 3; PDBTitle: crystal structure of the major allergen from fire ant2 venom, sol i 3 Phyre2 PDB 1xrd chain A domain 1 Region: 174 - 196 Aligned: 23 Modelled: 23 Confidence: 5.9% Identity: 26% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 3aqp chain B Region: 132 - 360 Aligned: 198 Modelled: 209 Confidence: 5.8% Identity: 15% PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus Phyre2 PDB 2cbi chain A domain 2 Region: 253 - 267 Aligned: 15 Modelled: 15 Confidence: 5.6% Identity: 27% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: alpha-D-glucuronidase/Hyaluronidase catalytic domain Phyre2 PDB 3dtu chain B domain 2 Region: 289 - 330 Aligned: 41 Modelled: 42 Confidence: 5.6% Identity: 12% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3b9e chain A Region: 305 - 328 Aligned: 24 Modelled: 24 Confidence: 5.5% Identity: 29% PDB header:hydrolase Chain: A: PDB Molecule:chitinase a; PDBTitle: crystal structure of inactive mutant e315m chitinase a from2 vibrio harveyi Phyre2 PDB 1bh9 chain B Region: 261 - 267 Aligned: 7 Modelled: 7 Confidence: 5.4% Identity: 43% Fold: Histone-fold Superfamily: Histone-fold Family: TBP-associated factors, TAFs Phyre2 1 c3quvB_ 2 c3dl8H_ 3 c2jxpA_ 4 d1p9pa_ 5 d1uala_ 6 c2akiY_ 7 d1o5ha_ 8 c3dinF_ 9 c3knuD_ 10 d2c42a2 11 c2zqpY_ 12 c3ky7A_ 13 c3j01A_ 14 c2vznA_ 15 d1xrda1 16 c3aqpB_ 17 d2cbia2 18 d3dtub2 19 c3b9eA_ 20 d1bh9b_ 21 22 23 24

Detailed template information

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

1 c3quvB_ 12.8 24 PDB header:transferase Chain: B: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: crystal structure of a trna-guanine-n1-methyltransferase from2 mycobacterium abscessus 2 c3dl8H_ 12.5 12 PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 3 c2jxpA_ 11.8 14 PDB header:lipoprotein Chain: A: PDB Molecule:putative lipoprotein b; PDBTitle: solution nmr structure of uncharacterized lipoprotein b2 from nitrosomonas europaea. northeast structural genomics3 target ner45a 4 d1p9pa_ 11.3 18 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:tRNA(m1G37)-methyltransferase TrmD 5 d1uala_ 10.7 21 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:tRNA(m1G37)-methyltransferase TrmD 6 c2akiY_ 10.6 13 PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli 7 d1o5ha_ 10.3 11 Fold:Methenyltetrahydrofolate cyclohydrolase-like Superfamily:Methenyltetrahydrofolate cyclohydrolase-like Family:Methenyltetrahydrofolate cyclohydrolase-like 8 c3dinF_ 10.1 14 PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase 9 c3knuD_ 7.5 25 PDB header:transferase Chain: D: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: crystal structure of trna (guanine-n1)-methyltransferase from2 anaplasma phagocytophilum 10 d2c42a2 7.5 31 Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:PFOR PP module 11 c2zqpY_ 7.3 13 PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: crystal structure of secye translocon from thermus2 thermophilus 12 c3ky7A_ 6.8 25 PDB header:transferase Chain: A: PDB Molecule:trna (guanine-n(1)-)-methyltransferase; PDBTitle: 2.35 angstrom resolution crystal structure of a putative trna2 (guanine-7-)-methyltransferase (trmd) from staphylococcus aureus3 subsp. aureus mrsa252 13 c3j01A_ 6.0 13 PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment 14 c2vznA_ 5.9 36 PDB header:allergen Chain: A: PDB Molecule:venom allergen 3; PDBTitle: crystal structure of the major allergen from fire ant2 venom, sol i 3 15 d1xrda1 5.9 26 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 16 c3aqpB_ 5.8 15 PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus 17 d2cbia2 5.6 27 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:alpha-D-glucuronidase/Hyaluronidase catalytic domain 18 d3dtub2 5.6 12 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 19 c3b9eA_ 5.5 29 PDB header:hydrolase Chain: A: PDB Molecule:chitinase a; PDBTitle: crystal structure of inactive mutant e315m chitinase a from2 vibrio harveyi 20 d1bh9b_ 5.4 43 Fold:Histone-fold Superfamily:Histone-fold Family:TBP-associated factors, TAFs 21 c3o7oB_ not modelled 5.3 50 PDB header:hydrolase Chain: B: PDB Molecule:endoglucanase; PDBTitle: use of synthetic symmetrization in the crystallization and structure2 determination of cela from thermotoga maritima 22 d1x7fa2 not modelled 5.3 50 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Outer surface protein, N-terminal domain 23 d2choa2 not modelled 5.2 27 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:alpha-D-glucuronidase/Hyaluronidase catalytic domain 24 c3rkoF_ not modelled 5.1 12 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution

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