Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	N	L	N	M	D	L	L	Y	M	A	A	A	V	M	M	G	L	A	A	I	G	A	A	I	G	I	G	I	L	G	G	K	F	L	E	G	A	A	R	Q	P	D	L	I	P	L	L	R	T	Q	F	F	I	V	M	G	L	V
Secondary structure
SS confidence
Disorder		?	?																																							?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.
Sequence		D	A	I	P	M	I	A	V	G	L	G	L	Y	V	M	F	A	V	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 1c99 chain A Region: 1 - 79 Aligned: 79 Modelled: 79 Confidence: 100.0% Identity: 100% Fold: Transmembrane helix hairpin Superfamily: F1F0 ATP synthase subunit C Family: F1F0 ATP synthase subunit C Phyre2 PDB 1wu0 chain A Region: 6 - 75 Aligned: 70 Modelled: 70 Confidence: 99.9% Identity: 44% PDB header:hydrolase Chain: A: PDB Molecule:atp synthase c chain; PDBTitle: solution structure of subunit c of f1fo-atp synthase from2 the thermophilic bacillus ps3 Phyre2 PDB 2x2v chain G Region: 10 - 76 Aligned: 67 Modelled: 67 Confidence: 99.9% Identity: 39% PDB header:membrane protein Chain: G: PDB Molecule:atp synthase subunit c; PDBTitle: structural basis of a novel proton-coordination type in an2 f1fo-atp synthase rotor ring Phyre2 PDB 2w5j chain M Region: 10 - 77 Aligned: 68 Modelled: 68 Confidence: 99.8% Identity: 31% PDB header:hydrolase Chain: M: PDB Molecule:atp synthase c chain, chloroplastic; PDBTitle: structure of the c14-rotor ring of the proton translocating2 chloroplast atp synthase Phyre2 PDB 1yce chain D Region: 10 - 77 Aligned: 67 Modelled: 68 Confidence: 99.8% Identity: 24% PDB header:membrane protein Chain: D: PDB Molecule:subunit c; PDBTitle: structure of the rotor ring of f-type na+-atpase from ilyobacter2 tartaricus Phyre2 PDB 2wpd chain P Region: 1 - 78 Aligned: 76 Modelled: 78 Confidence: 99.6% Identity: 21% PDB header:hydrolase Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial; PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase Phyre2 PDB 2xnd chain K Region: 10 - 76 Aligned: 66 Modelled: 67 Confidence: 99.5% Identity: 23% PDB header:hydrolase Chain: K: PDB Molecule:atp synthase lipid-binding protein, mitochondrial; PDBTitle: crystal structure of bovine f1-c8 sub-complex of atp2 synthase Phyre2 PDB 2bl2 chain F Region: 2 - 75 Aligned: 70 Modelled: 74 Confidence: 98.1% Identity: 13% PDB header:hydrolase Chain: F: PDB Molecule:v-type sodium atp synthase subunit k; PDBTitle: the membrane rotor of the v-type atpase from enterococcus2 hirae Phyre2 PDB 2qqp chain D Region: 24 - 42 Aligned: 19 Modelled: 19 Confidence: 12.5% Identity: 47% PDB header:virus Chain: D: PDB Molecule:small capsid protein; PDBTitle: crystal structure of authentic providence virus Phyre2 PDB 1cf2 chain O domain 1 Region: 26 - 45 Aligned: 20 Modelled: 20 Confidence: 11.1% Identity: 30% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain Phyre2 PDB 2voy chain D Region: 10 - 25 Aligned: 16 Modelled: 16 Confidence: 7.9% Identity: 50% PDB header:hydrolase Chain: D: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 1b7g chain O domain 1 Region: 26 - 45 Aligned: 20 Modelled: 20 Confidence: 7.7% Identity: 30% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain Phyre2 PDB 1cf2 chain Q Region: 26 - 45 Aligned: 20 Modelled: 20 Confidence: 7.4% Identity: 30% PDB header:oxidoreductase Chain: Q: PDB Molecule:protein (glyceraldehyde-3-phosphate PDBTitle: three-dimensional structure of d-glyceraldehyde-3-phosphate2 dehydrogenase from the hyperthermophilic archaeon3 methanothermus fervidus Phyre2 PDB 1r0k chain A domain 2 Region: 26 - 44 Aligned: 19 Modelled: 19 Confidence: 6.2% Identity: 32% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain Phyre2 PDB 2czc chain D Region: 27 - 45 Aligned: 19 Modelled: 19 Confidence: 6.0% Identity: 26% PDB header:oxidoreductase Chain: D: PDB Molecule:glyceraldehyde-3-phosphate dehydrogenase; PDBTitle: crystal structure of glyceraldehyde-3-phosphate dehydrogenase from2 pyrococcus horikoshii ot3 Phyre2 PDB 2bby chain A Region: 34 - 44 Aligned: 11 Modelled: 11 Confidence: 5.8% Identity: 36% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: DNA-binding domain from rap30 Phyre2 PDB 1b7g chain O Region: 27 - 45 Aligned: 19 Modelled: 19 Confidence: 5.4% Identity: 32% PDB header:oxidoreductase Chain: O: PDB Molecule:protein (glyceraldehyde 3-phosphate dehydrogenase); PDBTitle: glyceraldehyde 3-phosphate dehydrogenase Phyre2 PDB 1vjq chain B Region: 35 - 45 Aligned: 11 Modelled: 11 Confidence: 5.2% Identity: 55% PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. Phyre2 1 d1c99a_ 2 c1wu0A_ 3 c2x2vG_ 4 c2w5jM_ 5 c1yceD_ 6 c2wpdP_ 7 c2xndK_ 8 c2bl2F_ 9 c2qqpD_ 10 d1cf2o1 11 c2voyD_ 12 d1b7go1 13 c1cf2Q_ 14 d1r0ka2 15 c2czcD_ 16 d2bbya_ 17 c1b7gO_ 18 c1vjqB_

Detailed template information

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

1 d1c99a_ 100.0 100 Fold:Transmembrane helix hairpin Superfamily:F1F0 ATP synthase subunit C Family:F1F0 ATP synthase subunit C 2 c1wu0A_ 99.9 44 PDB header:hydrolase Chain: A: PDB Molecule:atp synthase c chain; PDBTitle: solution structure of subunit c of f1fo-atp synthase from2 the thermophilic bacillus ps3 3 c2x2vG_ 99.9 39 PDB header:membrane protein Chain: G: PDB Molecule:atp synthase subunit c; PDBTitle: structural basis of a novel proton-coordination type in an2 f1fo-atp synthase rotor ring 4 c2w5jM_ 99.8 31 PDB header:hydrolase Chain: M: PDB Molecule:atp synthase c chain, chloroplastic; PDBTitle: structure of the c14-rotor ring of the proton translocating2 chloroplast atp synthase 5 c1yceD_ 99.8 24 PDB header:membrane protein Chain: D: PDB Molecule:subunit c; PDBTitle: structure of the rotor ring of f-type na+-atpase from ilyobacter2 tartaricus 6 c2wpdP_ 99.6 21 PDB header:hydrolase Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial; PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase 7 c2xndK_ 99.5 23 PDB header:hydrolase Chain: K: PDB Molecule:atp synthase lipid-binding protein, mitochondrial; PDBTitle: crystal structure of bovine f1-c8 sub-complex of atp2 synthase 8 c2bl2F_ 98.1 13 PDB header:hydrolase Chain: F: PDB Molecule:v-type sodium atp synthase subunit k; PDBTitle: the membrane rotor of the v-type atpase from enterococcus2 hirae 9 c2qqpD_ 12.5 47 PDB header:virus Chain: D: PDB Molecule:small capsid protein; PDBTitle: crystal structure of authentic providence virus 10 d1cf2o1 11.1 30 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 11 c2voyD_ 7.9 50 PDB header:hydrolase Chain: D: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 12 d1b7go1 7.7 30 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 13 c1cf2Q_ 7.4 30 PDB header:oxidoreductase Chain: Q: PDB Molecule:protein (glyceraldehyde-3-phosphate PDBTitle: three-dimensional structure of d-glyceraldehyde-3-phosphate2 dehydrogenase from the hyperthermophilic archaeon3 methanothermus fervidus 14 d1r0ka2 6.2 32 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 15 c2czcD_ 6.0 26 PDB header:oxidoreductase Chain: D: PDB Molecule:glyceraldehyde-3-phosphate dehydrogenase; PDBTitle: crystal structure of glyceraldehyde-3-phosphate dehydrogenase from2 pyrococcus horikoshii ot3 16 d2bbya_ 5.8 36 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DNA-binding domain from rap30 17 c1b7gO_ 5.4 32 PDB header:oxidoreductase Chain: O: PDB Molecule:protein (glyceraldehyde 3-phosphate dehydrogenase); PDBTitle: glyceraldehyde 3-phosphate dehydrogenase 18 c1vjqB_ 5.2 55 PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability.

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