Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	R	I	V	S	S	S	H	D	R	T	S	L	L	S	T	H	K	V	L	R	N	T	Y	F	L	L	S	L	T	L	A	F	S	A	I	T	A	T	A	S	T	V	L	M	L	P	S	P	G	L	I	L	T	L	V	G	M	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?																																			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	L	M	F	L	T	Y	K	T	A	N	K	P	T	G	I	I	S	A	F	A	F	T	G	F	L	G	Y	I	L	G	P	I	L	N	T	Y	L	S	A	G	M	G	D	V	I	A	M	A	L	G	G	T	A	L	V	F	F	C	C
Secondary structure
SS confidence
Disorder									?	?	?	?	?	?	?																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	A	Y	V	L	T	T	R	K	D	M	S	F	L	G	G	M	L	M	A	G	I	V	V	V	L	I	G	M	V	A	N	I	F	L	Q	L	P	A	L	H	L	A	I	S	A	V	F	I	L	I	S	S	G	A	I	L	F	E	T
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.
Sequence		S	N	I	I	H	G	G	E	T	N	Y	I	R	A	T	V	S	L	Y	V	S	L	Y	N	I	F	V	S	L	L	S	I	L	G	F	A	S	R	D
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 3k07 chain A Region: 14 - 151 Aligned: 138 Modelled: 138 Confidence: 25.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa Phyre2 PDB 1iwg chain A domain 7 Region: 2 - 153 Aligned: 152 Modelled: 152 Confidence: 16.3% Identity: 7% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1oy8 chain A Region: 13 - 153 Aligned: 141 Modelled: 141 Confidence: 9.7% Identity: 5% PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump Phyre2 PDB 2e76 chain D Region: 13 - 46 Aligned: 34 Modelled: 34 Confidence: 8.9% Identity: 9% PDB header:photosynthesis Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus Phyre2 PDB 1iwg chain A domain 8 Region: 5 - 150 Aligned: 146 Modelled: 146 Confidence: 7.3% Identity: 12% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 2caz chain A domain 1 Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 7.1% Identity: 15% Fold: Long alpha-hairpin Superfamily: Endosomal sorting complex assembly domain Family: VPS23 C-terminal domain Phyre2 PDB 2h3o chain A Region: 115 - 130 Aligned: 16 Modelled: 16 Confidence: 7.1% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices Phyre2 PDB 2caz chain D Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 6.8% Identity: 15% PDB header:protein transport Chain: D: PDB Molecule:suppressor protein stp22 of temperature- PDBTitle: escrt-i core Phyre2 PDB 2f6m chain A domain 1 Region: 10 - 23 Aligned: 14 Modelled: 14 Confidence: 6.7% Identity: 14% Fold: Long alpha-hairpin Superfamily: Endosomal sorting complex assembly domain Family: VPS23 C-terminal domain Phyre2 PDB 1waz chain A Region: 113 - 130 Aligned: 18 Modelled: 18 Confidence: 5.8% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles Phyre2 1 c3k07A_ 2 d1iwga7 3 c1oy8A_ 4 c2e76D_ 5 d1iwga8 6 d2caza1 7 c2h3oA_ 8 c2cazD_ 9 d2f6ma1 10 c1wazA_

Detailed template information

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

1 c3k07A_ 25.0 11 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa 2 d1iwga7 16.3 7 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 3 c1oy8A_ 9.7 5 PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump 4 c2e76D_ 8.9 9 PDB header:photosynthesis Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus 5 d1iwga8 7.3 12 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 6 d2caza1 7.1 15 Fold:Long alpha-hairpin Superfamily:Endosomal sorting complex assembly domain Family:VPS23 C-terminal domain 7 c2h3oA_ 7.1 13 PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices 8 c2cazD_ 6.8 15 PDB header:protein transport Chain: D: PDB Molecule:suppressor protein stp22 of temperature- PDBTitle: escrt-i core 9 d2f6ma1 6.7 14 Fold:Long alpha-hairpin Superfamily:Endosomal sorting complex assembly domain Family:VPS23 C-terminal domain 10 c1wazA_ 5.8 11 PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles

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