Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	N	A	Q	E	A	V	K	T	R	H	K	E	T	S	L	I	F	P	V	L	A	L	V	V	L	F	L	W	G	S	S	Q	T	L	P	V	V	I	A	I	N	L	L	A	L	I	G	I	L	S	S	A	F	S	V	V	R	H
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	D	V	L	A	H	R	L	G	E	P	Y	G	S	L	I	L	S	L	S	V	V	I	L	E	V	S	L	I	S	A	L	M	A	T	G	D	A	A	P	T	L	M	R	D	T	L	Y	S	I	I	M	I	V	T	G	G	L	V	G
Secondary structure
SS confidence
Disorder																																				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	S	L	L	L	G	G	R	K	F	A	T	Q	Y	M	N	L	F	G	I	K	Q	Y	L	I	A	L	F	P	L	A	I	I	V	L	V	F	P	M	A	L	P	A	A	N	F	S	T	G	Q	A	L	L	V	A	L	I	S	A	A
Secondary structure
SS confidence
Disorder																																						?			?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		M	Y	G	V	F	L	L	I	Q	T	K	T	H	Q	S	L	F	V	Y	E	H	E	D	D	S	D	D	D	D	P	H	H	G	K	P	S	A	H	S	S	L	W	H	A	I	W	L	I	I	H	L	I	A	V	I	A	V	T	K	M
Secondary structure
SS confidence
Disorder													?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		N	A	S	S	L	E	T	L	L	D	S	M	N	A	P	V	A	F	T	G	F	L	V	A	L	L	I	L	S	P	E	G	L	G	A	L	K	A	V	L	N	N	Q	V	Q	R	A	M	N	L	F	F	G	S	V	L	A	T	I	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		L	T	V	P	V	V	T	L	I	A	F	M	T	G	N	E	L	Q	F	A	L	G	A	P	E	M	V	V	M	V	A	S	L	V	L	C	H	I	S	F	S	T	G	R	T	N	V	L	N	G	A	A	H	L	A	L	F	A	A	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.
Sequence		L	M	T	I	F	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 1xrd chain A domain 1 Region: 323 - 350 Aligned: 28 Modelled: 28 Confidence: 55.8% Identity: 32% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 3rko chain M Region: 111 - 252 Aligned: 139 Modelled: 142 Confidence: 24.2% Identity: 9% PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2oar chain A domain 1 Region: 279 - 310 Aligned: 32 Modelled: 32 Confidence: 23.3% Identity: 22% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2oar chain A Region: 277 - 310 Aligned: 34 Modelled: 34 Confidence: 15.9% Identity: 18% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 3mk7 chain F Region: 171 - 236 Aligned: 66 Modelled: 66 Confidence: 12.2% Identity: 6% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 1twf chain C domain 2 Region: 62 - 69 Aligned: 8 Modelled: 8 Confidence: 7.8% Identity: 63% Fold: Insert subdomain of RNA polymerase alpha subunit Superfamily: Insert subdomain of RNA polymerase alpha subunit Family: Insert subdomain of RNA polymerase alpha subunit Phyre2 PDB 1wgl chain A Region: 270 - 293 Aligned: 24 Modelled: 24 Confidence: 6.3% Identity: 13% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: CUE domain Phyre2 1 d1xrda1 2 c3rkoM_ 3 d2oara1 4 c2oarA_ 5 c3mk7F_ 6 d1twfc2 7 d1wgla_

Detailed template information

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

1 d1xrda1 55.8 32 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 2 c3rkoM_ 24.2 9 PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 3 d2oara1 23.3 22 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 4 c2oarA_ 15.9 18 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 5 c3mk7F_ 12.2 6 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 6 d1twfc2 7.8 63 Fold:Insert subdomain of RNA polymerase alpha subunit Superfamily:Insert subdomain of RNA polymerase alpha subunit Family:Insert subdomain of RNA polymerase alpha subunit 7 d1wgla_ 6.3 13 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:CUE domain

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

---

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