Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	S	M	D	K	L	T	T	G	V	A	Y	G	T	S	A	G	S	A	G	Y	W	F	L	Q	L	L	D	K	V	T	P	S	Q	W	A	A	I	G	V	L	G	S	L	V	F	G	L	L	T	Y	L	T	N	L	Y	F	K	I
Secondary structure
SS confidence
Disorder		?	?	?	?										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.
Sequence		K	E	D	K	R	K	A	A	R	G	E
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 2l2t chain A Region: 38 - 68 Aligned: 31 Modelled: 31 Confidence: 32.0% Identity: 26% 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 2qjx chain A Region: 2 - 34 Aligned: 22 Modelled: 33 Confidence: 24.2% Identity: 32% PDB header:protein binding Chain: A: PDB Molecule:protein bim1; PDBTitle: structural basis of microtubule plus end tracking by2 xmap215, clip-170 and eb1 Phyre2 PDB 3kdp chain G Region: 43 - 56 Aligned: 14 Modelled: 14 Confidence: 23.1% Identity: 36% 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 3kdp chain H Region: 43 - 56 Aligned: 14 Modelled: 14 Confidence: 23.1% Identity: 36% 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 1wyo chain A Region: 2 - 34 Aligned: 22 Modelled: 33 Confidence: 16.9% Identity: 32% PDB header:structural protein Chain: A: PDB Molecule:microtubule-associated protein rp/eb family PDBTitle: solution structure of the ch domain of human microtubule-2 associated protein rp/eb family member 3 Phyre2 PDB 2gbs chain A domain 1 Region: 31 - 45 Aligned: 15 Modelled: 15 Confidence: 11.3% Identity: 33% Fold: PUA domain-like Superfamily: PUA domain-like Family: Atu2648/PH1033-like Phyre2 PDB 2qjz chain A domain 1 Region: 2 - 35 Aligned: 23 Modelled: 23 Confidence: 10.2% Identity: 30% Fold: CH domain-like Superfamily: Calponin-homology domain, CH-domain Family: Calponin-homology domain, CH-domain Phyre2 PDB 3ixz chain B Region: 32 - 53 Aligned: 22 Modelled: 22 Confidence: 10.1% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:potassium-transporting atpase subunit beta; PDBTitle: pig gastric h+/k+-atpase complexed with aluminium fluoride Phyre2 PDB 3bq9 chain A Region: 53 - 71 Aligned: 19 Modelled: 19 Confidence: 9.7% Identity: 32% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted rossmann fold nucleotide-binding domain- PDBTitle: crystal structure of predicted nucleotide-binding protein from2 idiomarina baltica os145 Phyre2 PDB 3o0r chain C Region: 31 - 50 Aligned: 20 Modelled: 20 Confidence: 9.6% Identity: 35% PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment Phyre2 PDB 1m56 chain D Region: 36 - 50 Aligned: 15 Modelled: 15 Confidence: 9.5% Identity: 40% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 2kdn chain A Region: 28 - 39 Aligned: 12 Modelled: 12 Confidence: 9.2% Identity: 17% PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein pfe0790c; PDBTitle: solution structure of pfe0790c, a putative bola-like2 protein from the protozoan parasite plasmodium falciparum. Phyre2 PDB 1v5k chain A Region: 2 - 34 Aligned: 22 Modelled: 33 Confidence: 8.9% Identity: 32% Fold: CH domain-like Superfamily: Calponin-homology domain, CH-domain Family: Calponin-homology domain, CH-domain Phyre2 PDB 3b8e chain B Region: 32 - 53 Aligned: 22 Modelled: 22 Confidence: 8.8% Identity: 23% PDB header:hydrolase/transport protein Chain: B: PDB Molecule:sodium/potassium-transporting atpase subunit PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 1eys chain H domain 2 Region: 56 - 65 Aligned: 10 Modelled: 10 Confidence: 8.7% Identity: 40% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 3dl8 chain D Region: 41 - 58 Aligned: 18 Modelled: 18 Confidence: 8.7% Identity: 28% PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 3o2e chain A Region: 31 - 38 Aligned: 8 Modelled: 8 Confidence: 7.7% Identity: 50% PDB header:unknown function Chain: A: PDB Molecule:bola-like protein; PDBTitle: crystal structure of a bol-like protein from babesia bovis Phyre2 PDB 2veq chain A Region: 38 - 63 Aligned: 26 Modelled: 26 Confidence: 7.5% Identity: 31% PDB header:cell cycle Chain: A: PDB Molecule:centromere dna-binding protein complex cbf3 PDBTitle: insights into kinetochore-dna interactions from the2 structure of cep3p Phyre2 PDB 1ny8 chain A Region: 31 - 39 Aligned: 9 Modelled: 9 Confidence: 7.3% Identity: 44% Fold: Alpha-lytic protease prodomain-like Superfamily: BolA-like Family: BolA-like Phyre2 PDB 1v9j chain A Region: 31 - 38 Aligned: 8 Modelled: 8 Confidence: 6.8% Identity: 50% Fold: Alpha-lytic protease prodomain-like Superfamily: BolA-like Family: BolA-like Phyre2 1 c2l2tA_ 2 c2qjxA_ 3 c3kdpG_ 4 c3kdpH_ 5 c1wyoA_ 6 d2gbsa1 7 d2qjza1 8 c3ixzB_ 9 c3bq9A_ 10 c3o0rC_ 11 d1m56d_ 12 c2kdnA_ 13 d1v5ka_ 14 c3b8eB_ 15 d1eysh2 16 c3dl8D_ 17 c3o2eA_ 18 c2veqA_ 19 d1ny8a_ 20 d1v9ja_ 21 22 23

Detailed template information

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

1 c2l2tA_ 32.0 26 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 2 c2qjxA_ 24.2 32 PDB header:protein binding Chain: A: PDB Molecule:protein bim1; PDBTitle: structural basis of microtubule plus end tracking by2 xmap215, clip-170 and eb1 3 c3kdpG_ 23.1 36 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 4 c3kdpH_ 23.1 36 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 5 c1wyoA_ 16.9 32 PDB header:structural protein Chain: A: PDB Molecule:microtubule-associated protein rp/eb family PDBTitle: solution structure of the ch domain of human microtubule-2 associated protein rp/eb family member 3 6 d2gbsa1 11.3 33 Fold:PUA domain-like Superfamily:PUA domain-like Family:Atu2648/PH1033-like 7 d2qjza1 10.2 30 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 8 c3ixzB_ 10.1 18 PDB header:hydrolase Chain: B: PDB Molecule:potassium-transporting atpase subunit beta; PDBTitle: pig gastric h+/k+-atpase complexed with aluminium fluoride 9 c3bq9A_ 9.7 32 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted rossmann fold nucleotide-binding domain- PDBTitle: crystal structure of predicted nucleotide-binding protein from2 idiomarina baltica os145 10 c3o0rC_ 9.6 35 PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment 11 d1m56d_ 9.5 40 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 12 c2kdnA_ 9.2 17 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein pfe0790c; PDBTitle: solution structure of pfe0790c, a putative bola-like2 protein from the protozoan parasite plasmodium falciparum. 13 d1v5ka_ 8.9 32 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 14 c3b8eB_ 8.8 23 PDB header:hydrolase/transport protein Chain: B: PDB Molecule:sodium/potassium-transporting atpase subunit PDBTitle: crystal structure of the sodium-potassium pump 15 d1eysh2 8.7 40 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 16 c3dl8D_ 8.7 28 PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 17 c3o2eA_ 7.7 50 PDB header:unknown function Chain: A: PDB Molecule:bola-like protein; PDBTitle: crystal structure of a bol-like protein from babesia bovis 18 c2veqA_ 7.5 31 PDB header:cell cycle Chain: A: PDB Molecule:centromere dna-binding protein complex cbf3 PDBTitle: insights into kinetochore-dna interactions from the2 structure of cep3p 19 d1ny8a_ 7.3 44 Fold:Alpha-lytic protease prodomain-like Superfamily:BolA-like Family:BolA-like 20 d1v9ja_ 6.8 50 Fold:Alpha-lytic protease prodomain-like Superfamily:BolA-like Family:BolA-like 21 c3eopB_ not modelled 6.5 20 PDB header:unknown function Chain: B: PDB Molecule:thymocyte nuclear protein 1; PDBTitle: crystal structure of the duf55 domain of human thymocyte nuclear2 protein 1 22 c3htuE_ not modelled 5.7 25 PDB header:protein transport Chain: E: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: crystal structure of the human vps25-vps20 subcomplex 23 d1vk5a_ not modelled 5.5 36 Fold:Hypothetical protein At3g22680 Superfamily:Hypothetical protein At3g22680 Family:Hypothetical protein At3g22680

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