Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	N	L	W	M	F	L	A	L	C	I	V	C	V	S	G	Y	I	G	Q	V	L	N	V	V	S	A	V	S	S	F	F	G	M	V	I	L	A	A	L	I	Y	Y	F	T	M	W	L	T	G	G	N	E	L	V	T	G	I	F
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80
Sequence		M	F	L	A	P	A	C	G	L	M	I	R	F	M	V	G	Y	G	R	R
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 1v29 chain A Region: 8 - 24 Aligned: 16 Modelled: 17 Confidence: 23.7% Identity: 31% Fold: Nitrile hydratase alpha chain Superfamily: Nitrile hydratase alpha chain Family: Nitrile hydratase alpha chain Phyre2 PDB 3mp7 chain B Region: 56 - 77 Aligned: 21 Modelled: 22 Confidence: 23.5% Identity: 38% PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes Phyre2 PDB 2f93 chain B domain 1 Region: 27 - 38 Aligned: 12 Modelled: 12 Confidence: 15.0% Identity: 50% Fold: Transmembrane helix hairpin Superfamily: Htr2 transmembrane domain-like Family: Htr2 transmembrane domain-like Phyre2 PDB 2f93 chain B Region: 27 - 38 Aligned: 12 Modelled: 12 Confidence: 15.0% Identity: 50% PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: k intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure Phyre2 PDB 2f95 chain B Region: 27 - 38 Aligned: 12 Modelled: 12 Confidence: 13.8% Identity: 50% PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: m intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure Phyre2 PDB 1h2s chain B Region: 27 - 38 Aligned: 12 Modelled: 12 Confidence: 11.6% Identity: 50% Fold: Transmembrane helix hairpin Superfamily: Htr2 transmembrane domain-like Family: Htr2 transmembrane domain-like Phyre2 PDB 1h2s chain B Region: 27 - 38 Aligned: 12 Modelled: 12 Confidence: 11.6% Identity: 50% PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: molecular basis of transmenbrane signalling by sensory2 rhodopsin ii-transducer complex Phyre2 PDB 2ftx chain B domain 1 Region: 15 - 24 Aligned: 10 Modelled: 10 Confidence: 7.9% Identity: 30% Fold: Kinetochore globular domain-like Superfamily: Kinetochore globular domain Family: Spc24-like Phyre2 PDB 2fv4 chain B Region: 15 - 24 Aligned: 10 Modelled: 10 Confidence: 7.8% Identity: 30% PDB header:structural protein, protein binding Chain: B: PDB Molecule:hypothetical 24.6 kda protein in ilv2-ade17 PDBTitle: nmr solution structure of the yeast kinetochore spc24/spc252 globular domain Phyre2 PDB 2k1a chain A Region: 25 - 43 Aligned: 19 Modelled: 19 Confidence: 5.8% Identity: 21% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 1rzh chain H domain 2 Region: 25 - 45 Aligned: 19 Modelled: 21 Confidence: 5.3% Identity: 47% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 2p41 chain A domain 1 Region: 14 - 33 Aligned: 20 Modelled: 20 Confidence: 5.3% Identity: 25% Fold: S-adenosyl-L-methionine-dependent methyltransferases Superfamily: S-adenosyl-L-methionine-dependent methyltransferases Family: mRNA cap methylase Phyre2 1 d1v29a_ 2 c3mp7B_ 3 d2f93b1 4 c2f93B_ 5 c2f95B_ 6 d1h2sb_ 7 c1h2sB_ 8 d2ftxb1 9 c2fv4B_ 10 c2k1aA_ 11 d1rzhh2 12 d2p41a1

Detailed template information

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

1 d1v29a_ 23.7 31 Fold:Nitrile hydratase alpha chain Superfamily:Nitrile hydratase alpha chain Family:Nitrile hydratase alpha chain 2 c3mp7B_ 23.5 38 PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes 3 d2f93b1 15.0 50 Fold:Transmembrane helix hairpin Superfamily:Htr2 transmembrane domain-like Family:Htr2 transmembrane domain-like 4 c2f93B_ 15.0 50 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: k intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure 5 c2f95B_ 13.8 50 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: m intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure 6 d1h2sb_ 11.6 50 Fold:Transmembrane helix hairpin Superfamily:Htr2 transmembrane domain-like Family:Htr2 transmembrane domain-like 7 c1h2sB_ 11.6 50 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: molecular basis of transmenbrane signalling by sensory2 rhodopsin ii-transducer complex 8 d2ftxb1 7.9 30 Fold:Kinetochore globular domain-like Superfamily:Kinetochore globular domain Family:Spc24-like 9 c2fv4B_ 7.8 30 PDB header:structural protein, protein binding Chain: B: PDB Molecule:hypothetical 24.6 kda protein in ilv2-ade17 PDBTitle: nmr solution structure of the yeast kinetochore spc24/spc252 globular domain 10 c2k1aA_ 5.8 21 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 11 d1rzhh2 5.3 47 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 12 d2p41a1 5.3 25 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:mRNA cap methylase

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