Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	N	N	T	T	G	F	T	R	I	I	K	A	A	G	Y	S	W	K	G	L	R	A	A	W	I	N	E	A	A	F	R	Q	E	G	V	A	V	L	L	A	V	V	I	A	C	W	L	D	V	D	A	I	T	R	V	L	L	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	S	V	M	L	V	M	I	V	E	I	L	N	S	A	I	E	A	V	V	D	R	I	G	S	E	Y	H	E	L	S	G	R	A	K	D	M	G	S	A	A	V	L	I	A	I	I	V	A	V	I	T	W	C	I	L	L	W	S	H
Secondary structure
SS confidence
Disorder																																																													?
Disorder confidence
		.	.
Sequence		F	G
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 2kdc chain C Region: 2 - 122 Aligned: 121 Modelled: 121 Confidence: 100.0% Identity: 100% PDB header:transferase Chain: C: PDB Molecule:diacylglycerol kinase; PDBTitle: nmr solution structure of e. coli diacylglycerol kinase2 (dagk) in dpc micelles Phyre2 PDB 1rhz chain B Region: 70 - 120 Aligned: 51 Modelled: 51 Confidence: 15.7% Identity: 16% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 1ik7 chain A Region: 60 - 91 Aligned: 32 Modelled: 32 Confidence: 13.5% Identity: 13% Fold: DEATH domain Superfamily: DEATH domain Family: DEATH domain, DD Phyre2 PDB 2y69 chain X Region: 84 - 112 Aligned: 28 Modelled: 29 Confidence: 12.6% Identity: 18% PDB header:electron transport Chain: X: PDB Molecule:cytochrome c oxidase polypeptide 7b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1v54 chain K Region: 84 - 112 Aligned: 28 Modelled: 29 Confidence: 12.6% Identity: 18% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIb Family: Mitochondrial cytochrome c oxidase subunit VIIb Phyre2 PDB 1rh5 chain B Region: 70 - 119 Aligned: 50 Modelled: 50 Confidence: 7.0% Identity: 16% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 2wwb chain B Region: 70 - 111 Aligned: 42 Modelled: 42 Confidence: 6.9% Identity: 12% PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome Phyre2 PDB 1p58 chain F Region: 23 - 66 Aligned: 44 Modelled: 44 Confidence: 6.4% Identity: 16% PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction Phyre2 PDB 3kdp chain H Region: 103 - 120 Aligned: 18 Modelled: 18 Confidence: 6.1% Identity: 39% PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 3kdp chain G Region: 103 - 120 Aligned: 18 Modelled: 18 Confidence: 6.1% Identity: 39% PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 2ww9 chain B Region: 70 - 111 Aligned: 42 Modelled: 42 Confidence: 6.0% Identity: 17% PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 1 c2kdcC_ 2 d1rhzb_ 3 d1ik7a_ 4 c2y69X_ 5 d1v54k_ 6 d1rh5b_ 7 c2wwbB_ 8 c1p58F_ 9 c3kdpH_ 10 c3kdpG_ 11 c2ww9B_

Detailed template information

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

1 c2kdcC_ 100.0 100 PDB header:transferase Chain: C: PDB Molecule:diacylglycerol kinase; PDBTitle: nmr solution structure of e. coli diacylglycerol kinase2 (dagk) in dpc micelles 2 d1rhzb_ 15.7 16 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 3 d1ik7a_ 13.5 13 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 4 c2y69X_ 12.6 18 PDB header:electron transport Chain: X: PDB Molecule:cytochrome c oxidase polypeptide 7b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 5 d1v54k_ 12.6 18 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIb Family:Mitochondrial cytochrome c oxidase subunit VIIb 6 d1rh5b_ 7.0 16 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 7 c2wwbB_ 6.9 12 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome 8 c1p58F_ 6.4 16 PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 9 c3kdpH_ 6.1 39 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 10 c3kdpG_ 6.1 39 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 11 c2ww9B_ 6.0 17 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome

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