Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	Y	I	D	K	A	T	I	L	K	F	D	L	E	M	L	K	K	H	R	R	A	I	Q	F	I	A	V	L	L	F	I	V	G	L	L	C	I	S	F	P	F	V	S	G	D	I	L	S	T	V	V	G	A	L	L	I	C	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?							?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	I	A	L	I	V	G	L	F	S	N	R	S	H	N	F	W	P	V	L	S	G	F	L	V	A	V	A	Y	L	L	I	G	Y	F	F	I	R	A	P	E	L	G	I	F	A	I	A	A	F	I	A	G	L	F	C	V	A	G	V
Secondary structure
SS confidence
Disorder												?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	R	L	M	S	W	Y	R	Q	R	S	M	K	G	S	W	L	Q	L	V	I	G	V	L	D	I	V	I	A	W	I	F	L	G	A	T	P	M	V	S	V	T	L	V	S	T	L	V	G	I	E	L	I	F	S	A	A	S	L	F
Secondary structure
SS confidence
Disorder													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190
Sequence		S	F	A	S	L	F	V	K	Q	Q
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 1s7b chain A Region: 83 - 185 Aligned: 99 Modelled: 103 Confidence: 16.3% Identity: 12% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 1r0k chain A domain 3 Region: 4 - 23 Aligned: 20 Modelled: 20 Confidence: 9.9% Identity: 30% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Dihydrodipicolinate reductase-like Phyre2 PDB 1q0q chain A domain 3 Region: 4 - 23 Aligned: 20 Modelled: 20 Confidence: 9.0% Identity: 25% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Dihydrodipicolinate reductase-like Phyre2 PDB 3m92 chain B Region: 3 - 24 Aligned: 22 Modelled: 22 Confidence: 8.5% Identity: 27% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ycin; PDBTitle: the structure of ycin, an unchracterized protein from shigella2 flexneri. Phyre2 PDB 1pk1 chain B Region: 3 - 20 Aligned: 18 Modelled: 18 Confidence: 6.6% Identity: 28% PDB header:transcription repression Chain: B: PDB Molecule:sex comb on midleg cg9495-pa; PDBTitle: hetero sam domain structure of ph and scm. Phyre2 PDB 1pk1 chain C domain 1 Region: 3 - 20 Aligned: 18 Modelled: 18 Confidence: 6.5% Identity: 22% Fold: SAM domain-like Superfamily: SAM/Pointed domain Family: SAM (sterile alpha motif) domain Phyre2 1 d1s7ba_ 2 d1r0ka3 3 d1q0qa3 4 c3m92B_ 5 c1pk1B_ 6 d1pk1c1

Detailed template information

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

1 d1s7ba_ 16.3 12 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 d1r0ka3 9.9 30 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 3 d1q0qa3 9.0 25 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 4 c3m92B_ 8.5 27 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ycin; PDBTitle: the structure of ycin, an unchracterized protein from shigella2 flexneri. 5 c1pk1B_ 6.6 28 PDB header:transcription repression Chain: B: PDB Molecule:sex comb on midleg cg9495-pa; PDBTitle: hetero sam domain structure of ph and scm. 6 d1pk1c1 6.5 22 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) 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