Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	L	N	T	L	I	S	Q	Y	G	Y	A	A	L	V	I	G	S	L	A	E	G	E	T	V	T	L	L	G	G	V	A	A	H	Q	G	L	L	K	F	P	L	V	V	L	S	V	A	L	G	G	M	I	G	D	Q	V	L	Y
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	C	G	R	R	F	G	G	K	L	L	R	R	F	S	K	H	Q	D	K	I	E	R	A	Q	K	L	I	Q	R	H	P	Y	L	F	V	I	G	T	R	F	M	Y	G	F	R	V	I	G	P	T	L	I	G	A	S	Q	L	P	P
Secondary structure
SS confidence
Disorder																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	I	F	L	P	L	N	I	L	G	A	F	A	W	A	L	I	F	T	T	I	G	Y	A	G	G	Q	V	I	A	P	W	L	H	N	L	D	Q	H	L	K	H	W	V	W	L	I	L	V	V	V	L	V	V	G	V	R	W	W	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.
Sequence		K	R	R	G	K	K	K	P	D	H	Q	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 2bbj chain B Region: 78 - 183 Aligned: 70 Modelled: 70 Confidence: 45.9% Identity: 13% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 2rdd chain B Region: 165 - 192 Aligned: 28 Modelled: 28 Confidence: 28.6% Identity: 25% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 1pw4 chain A Region: 93 - 190 Aligned: 98 Modelled: 98 Confidence: 14.4% Identity: 16% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2knc chain A Region: 133 - 191 Aligned: 40 Modelled: 40 Confidence: 12.6% Identity: 23% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2l2t chain A Region: 162 - 190 Aligned: 29 Modelled: 29 Confidence: 12.0% Identity: 17% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain Phyre2 PDB 3ehb chain B domain 2 Region: 147 - 191 Aligned: 45 Modelled: 45 Confidence: 10.0% Identity: 11% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1t33 chain A domain 2 Region: 52 - 91 Aligned: 40 Modelled: 40 Confidence: 9.1% Identity: 13% Fold: Tetracyclin repressor-like, C-terminal domain Superfamily: Tetracyclin repressor-like, C-terminal domain Family: Tetracyclin repressor-like, C-terminal domain Phyre2 PDB 3dtu chain B domain 2 Region: 147 - 191 Aligned: 45 Modelled: 45 Confidence: 8.5% Identity: 16% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1fft chain B domain 2 Region: 151 - 191 Aligned: 41 Modelled: 41 Confidence: 7.6% Identity: 10% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2oar chain A domain 1 Region: 162 - 192 Aligned: 31 Modelled: 31 Confidence: 7.0% Identity: 13% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 1 c2bbjB_ 2 c2rddB_ 3 d1pw4a_ 4 c2kncA_ 5 c2l2tA_ 6 d3ehbb2 7 d1t33a2 8 d3dtub2 9 d1fftb2 10 d2oara1

Detailed template information

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

1 c2bbjB_ 45.9 13 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 2 c2rddB_ 28.6 25 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 3 d1pw4a_ 14.4 16 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 4 c2kncA_ 12.6 23 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 5 c2l2tA_ 12.0 17 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 6 d3ehbb2 10.0 11 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 7 d1t33a2 9.1 13 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 8 d3dtub2 8.5 16 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 9 d1fftb2 7.6 10 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 10 d2oara1 7.0 13 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel

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