Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	D	L	F	K	A	I	G	L	G	L	V	V	L	L	P	L	A	N	P	L	T	T	V	A	L	F	L	G	L	A	G	N	M	N	S	A	E	R	N	R	Q	S	L	M	A	S	V	Y	V	F	A	I	M	M	V	A	Y	Y
Secondary structure
SS confidence
Disorder		?	?	?																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	G	Q	L	V	M	D	T	F	G	I	S	I	P	G	L	R	I	A	G	G	L	I	V	A	F	I	G	F	R	M	L	F	P	Q	Q	K	A	I	D	S	P	E	A	K	S	K	S	E	E	L	E	D	E	P	S	A	N	I	A
Secondary structure
SS confidence
Disorder																																	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	V	P	L	A	M	P	S	T	A	G	P	G	T	I	A	M	I	I	S	S	A	S	T	V	R	Q	S	S	T	F	A	D	W	V	L	M	V	A	P	P	L	I	F	F	L	V	A	V	I	L	W	G	S	L	R	S	S	G	A
Secondary structure
SS confidence
Disorder																								?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.
Sequence		I	M	R	L	V	G	K	G	G	I	E	A	I	S	R	L	M	G	F	L	L	V	C	M	G	V	Q	F	I	I	N	G	I	L	E	I	I	K	T	Y	H
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 3aqp chain B Region: 45 - 184 Aligned: 134 Modelled: 140 Confidence: 54.4% Identity: 9% 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 3k07 chain A Region: 45 - 191 Aligned: 145 Modelled: 147 Confidence: 51.3% Identity: 8% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa Phyre2 PDB 1oy8 chain A Region: 45 - 90 Aligned: 46 Modelled: 46 Confidence: 27.7% Identity: 20% 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 2vv5 chain D Region: 6 - 91 Aligned: 86 Modelled: 86 Confidence: 18.3% Identity: 6% PDB header:membrane protein Chain: D: PDB Molecule:small-conductance mechanosensitive channel; PDBTitle: the open structure of mscs Phyre2 PDB 1hji chain B Region: 33 - 54 Aligned: 22 Modelled: 22 Confidence: 14.7% Identity: 18% PDB header:bacteriophage hk022 Chain: B: PDB Molecule:nun-protein; PDBTitle: bacteriophage hk022 nun-protein-nutboxb-rna complex Phyre2 PDB 2nn6 chain H domain 3 Region: 33 - 74 Aligned: 42 Modelled: 42 Confidence: 7.6% Identity: 12% Fold: Eukaryotic type KH-domain (KH-domain type I) Superfamily: Eukaryotic type KH-domain (KH-domain type I) Family: Eukaryotic type KH-domain (KH-domain type I) Phyre2 PDB 2vv5 chain A domain 3 Region: 37 - 91 Aligned: 55 Modelled: 55 Confidence: 6.4% Identity: 5% Fold: Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily: Mechanosensitive channel protein MscS (YggB), transmembrane region Family: Mechanosensitive channel protein MscS (YggB), transmembrane region Phyre2 PDB 1iwg chain A domain 8 Region: 45 - 171 Aligned: 124 Modelled: 127 Confidence: 6.1% Identity: 8% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 1 c3aqpB_ 2 c3k07A_ 3 c1oy8A_ 4 c2vv5D_ 5 c1hjiB_ 6 d2nn6h3 7 d2vv5a3 8 d1iwga8

Detailed template information

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

1 c3aqpB_ 54.4 9 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 2 c3k07A_ 51.3 8 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa 3 c1oy8A_ 27.7 20 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 c2vv5D_ 18.3 6 PDB header:membrane protein Chain: D: PDB Molecule:small-conductance mechanosensitive channel; PDBTitle: the open structure of mscs 5 c1hjiB_ 14.7 18 PDB header:bacteriophage hk022 Chain: B: PDB Molecule:nun-protein; PDBTitle: bacteriophage hk022 nun-protein-nutboxb-rna complex 6 d2nn6h3 7.6 12 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 7 d2vv5a3 6.4 5 Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region Family:Mechanosensitive channel protein MscS (YggB), transmembrane region 8 d1iwga8 6.1 8 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane 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

---

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