Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.
Sequence		M	F	R	W	G	I	I	F	L	V	I	A	L	I	A	A	A	L	G	F	G	G	L	A	G	T	A	A	G	A	A	K	I	V	F	V	V	G	I	I	L	F	L	V	S	L	F	M	G	R	K	R	P
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 1ijd chain B Region: 7 - 20 Aligned: 14 Modelled: 14 Confidence: 19.6% Identity: 64% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1jb0 chain M Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 17.6% Identity: 67% PDB header:photosynthesis Chain: M: PDB Molecule:photosystem 1 reaction centre subunit xii; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria Phyre2 PDB 1jb0 chain M Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 17.6% Identity: 67% Fold: Single transmembrane helix Superfamily: Subunit XII of photosystem I reaction centre, PsaM Family: Subunit XII of photosystem I reaction centre, PsaM Phyre2 PDB 2iub chain A domain 2 Region: 4 - 36 Aligned: 33 Modelled: 33 Confidence: 15.3% Identity: 24% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 1xme chain B domain 2 Region: 2 - 15 Aligned: 14 Modelled: 14 Confidence: 12.2% Identity: 50% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2ari chain A Region: 15 - 31 Aligned: 17 Modelled: 17 Confidence: 9.2% Identity: 59% PDB header:viral protein Chain: A: PDB Molecule:envelope polyprotein gp160; PDBTitle: solution structure of micelle-bound fusion domain of hiv-12 gp41 Phyre2 PDB 2klu chain A Region: 16 - 36 Aligned: 21 Modelled: 21 Confidence: 8.2% Identity: 29% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 1rh1 chain A domain 2 Region: 3 - 39 Aligned: 37 Modelled: 37 Confidence: 7.3% Identity: 24% Fold: Toxins' membrane translocation domains Superfamily: Colicin Family: Colicin Phyre2 PDB 1erf chain A Region: 15 - 31 Aligned: 17 Modelled: 17 Confidence: 6.1% Identity: 53% PDB header:viral protein Chain: A: PDB Molecule:transmembrane glycoprotein; PDBTitle: conformational mapping of the n-terminal fusion peptide of2 hiv-1 gp41 using 13c-enhanced fourier transform infrared3 spectroscopy (ftir) Phyre2 PDB 2j7a chain C Region: 8 - 29 Aligned: 22 Modelled: 22 Confidence: 6.0% Identity: 5% PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome c quinol dehydrogenase nrfh; PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex from desulfovibrio vulgaris Phyre2 PDB 3m7b chain A Region: 15 - 48 Aligned: 34 Modelled: 34 Confidence: 5.8% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:tellurite resistance protein teha homolog; PDBTitle: crystal structure of plant slac1 homolog teha Phyre2 PDB 1cii chain A Region: 16 - 49 Aligned: 30 Modelled: 34 Confidence: 5.8% Identity: 27% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 2bbj chain B Region: 4 - 38 Aligned: 35 Modelled: 35 Confidence: 5.6% Identity: 26% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 1 d1ijdb_ 2 c1jb0M_ 3 d1jb0m_ 4 d2iuba2 5 d1xmeb2 6 c2ariA_ 7 c2kluA_ 8 d1rh1a2 9 c1erfA_ 10 c2j7aC_ 11 c3m7bA_ 12 c1ciiA_ 13 c2bbjB_

Detailed template information

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

1 d1ijdb_ 19.6 64 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 2 c1jb0M_ 17.6 67 PDB header:photosynthesis Chain: M: PDB Molecule:photosystem 1 reaction centre subunit xii; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 3 d1jb0m_ 17.6 67 Fold:Single transmembrane helix Superfamily:Subunit XII of photosystem I reaction centre, PsaM Family:Subunit XII of photosystem I reaction centre, PsaM 4 d2iuba2 15.3 24 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 5 d1xmeb2 12.2 50 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 6 c2ariA_ 9.2 59 PDB header:viral protein Chain: A: PDB Molecule:envelope polyprotein gp160; PDBTitle: solution structure of micelle-bound fusion domain of hiv-12 gp41 7 c2kluA_ 8.2 29 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 8 d1rh1a2 7.3 24 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 9 c1erfA_ 6.1 53 PDB header:viral protein Chain: A: PDB Molecule:transmembrane glycoprotein; PDBTitle: conformational mapping of the n-terminal fusion peptide of2 hiv-1 gp41 using 13c-enhanced fourier transform infrared3 spectroscopy (ftir) 10 c2j7aC_ 6.0 5 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome c quinol dehydrogenase nrfh; PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex from desulfovibrio vulgaris 11 c3m7bA_ 5.8 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:tellurite resistance protein teha homolog; PDBTitle: crystal structure of plant slac1 homolog teha 12 c1ciiA_ 5.8 27 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 13 c2bbjB_ 5.6 26 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter

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