Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	T	S	L	F	K	S	L	Y	F	Q	V	L	T	A	I	A	I	G	I	L	L	G	H	F	Y	P	E	I	G	E	Q	M	K	P	L	G	D	G	F	V	K	L	I	K	M	I	I	A	P	V	I	F	C	T	V	V	T	G
Secondary structure
SS confidence
Disorder		?	?	?	?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	A	G	M	E	S	M	K	A	V	G	R	T	G	A	V	A	L	L	Y	F	E	I	V	S	T	I	A	L	I	I	G	L	I	I	V	N	V	V	Q	P	G	A	G	M	N	V	D	P	A	T	L	D	A	K	A	V	A	V	Y
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?	?																																			?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	D	Q	A	K	D	Q	G	I	V	A	F	I	M	D	V	I	P	A	S	V	I	G	A	F	A	S	G	N	I	L	Q	V	L	L	F	A	V	L	F	G	F	A	L	H	R	L	G	S	K	G	Q	L	I	F	N	V	I	E	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																	?	?	?																				?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	S	Q	V	I	F	G	I	I	N	M	I	M	R	L	A	P	I	G	A	F	G	A	M	A	F	T	I	G	K	Y	G	V	G	T	L	V	Q	L	G	Q	L	I	I	C	F	Y	I	T	C	I	L	F	V	V	L	V	L	G	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	A	K	A	T	G	F	S	I	F	K	F	I	R	Y	I	R	E	E	L	L	I	V	L	G	T	S	S	S	E	S	A	L	P	R	M	L	D	K	M	E	K	L	G	C	R	K	S	V	V	G	L	V	I	P	T	G	Y	S	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		N	L	D	G	T	S	I	Y	L	T	M	A	A	V	F	I	A	Q	A	T	N	S	Q	M	D	I	V	H	Q	I	T	L	L	I	V	L	L	L	S	S	K	G	A	A	G	V	T	G	S	G	F	I	V	L	A	A	T	L	S	A
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		V	G	H	L	P	V	A	G	L	A	L	I	L	G	I	D	R	F	M	S	E	A	R	A	L	T	N	L	V	G	N	G	V	A	T	I	V	V	A	K	W	V	K	E	L	D	H	K	K	L	D	D	V	L	N	N	R	A	P	D
Secondary structure
SS confidence
Disorder		?		?	?																																									?							?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		G	K	T	H	E	L	S	S
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 2nww chain A domain 1 Region: 12 - 402 Aligned: 382 Modelled: 391 Confidence: 100.0% Identity: 31% Fold: Proton glutamate symport protein Superfamily: Proton glutamate symport protein Family: Proton glutamate symport protein Phyre2 PDB 1a77 chain A domain 1 Region: 324 - 362 Aligned: 38 Modelled: 39 Confidence: 42.4% Identity: 18% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1mc8 chain A domain 1 Region: 324 - 364 Aligned: 40 Modelled: 41 Confidence: 23.3% Identity: 18% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1ul1 chain X domain 1 Region: 324 - 364 Aligned: 39 Modelled: 41 Confidence: 21.2% Identity: 15% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1b43 chain A domain 1 Region: 324 - 362 Aligned: 38 Modelled: 39 Confidence: 18.4% Identity: 16% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1iwg chain A domain 8 Region: 149 - 251 Aligned: 103 Modelled: 103 Confidence: 16.5% Identity: 13% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 3ah5 chain E Region: 278 - 302 Aligned: 25 Modelled: 25 Confidence: 15.0% Identity: 12% PDB header:transferase Chain: E: PDB Molecule:thymidylate synthase thyx; PDBTitle: crystal structure of flavin dependent thymidylate synthase thyx from2 helicobacter pylori complexed with fad and dump Phyre2 PDB 1rxw chain A domain 1 Region: 324 - 362 Aligned: 37 Modelled: 39 Confidence: 13.8% Identity: 19% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1xo1 chain A domain 1 Region: 325 - 369 Aligned: 43 Modelled: 45 Confidence: 11.5% Identity: 21% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1o26 chain A Region: 278 - 298 Aligned: 21 Modelled: 21 Confidence: 11.3% Identity: 19% Fold: Thymidylate synthase-complementing protein Thy1 Superfamily: Thymidylate synthase-complementing protein Thy1 Family: Thymidylate synthase-complementing protein Thy1 Phyre2 PDB 3aqp chain B Region: 149 - 247 Aligned: 97 Modelled: 99 Confidence: 10.0% Identity: 11% 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 3dl8 chain D Region: 150 - 181 Aligned: 32 Modelled: 32 Confidence: 9.4% Identity: 25% PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 1cmw chain A domain 1 Region: 324 - 364 Aligned: 41 Modelled: 41 Confidence: 7.0% Identity: 20% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 1 d2nwwa1 2 d1a77a1 3 d1mc8a1 4 d1ul1x1 5 d1b43a1 6 d1iwga8 7 c3ah5E_ 8 d1rxwa1 9 d1xo1a1 10 d1o26a_ 11 c3aqpB_ 12 c3dl8D_ 13 d1cmwa1

Detailed template information

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

1 d2nwwa1 100.0 31 Fold:Proton glutamate symport protein Superfamily:Proton glutamate symport protein Family:Proton glutamate symport protein 2 d1a77a1 42.4 18 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 3 d1mc8a1 23.3 18 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 4 d1ul1x1 21.2 15 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 5 d1b43a1 18.4 16 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 6 d1iwga8 16.5 13 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 7 c3ah5E_ 15.0 12 PDB header:transferase Chain: E: PDB Molecule:thymidylate synthase thyx; PDBTitle: crystal structure of flavin dependent thymidylate synthase thyx from2 helicobacter pylori complexed with fad and dump 8 d1rxwa1 13.8 19 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 9 d1xo1a1 11.5 21 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 10 d1o26a_ 11.3 19 Fold:Thymidylate synthase-complementing protein Thy1 Superfamily:Thymidylate synthase-complementing protein Thy1 Family:Thymidylate synthase-complementing protein Thy1 11 c3aqpB_ 10.0 11 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 12 c3dl8D_ 9.4 25 PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 13 d1cmwa1 7.0 20 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain

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