Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	N	M	F	E	P	P	K	N	Y	N	E	M	L	P	K	L	H	K	A	T	F	L	N	T	L	I	Y	C	I	L	L	V	I	Y	E	Y	I	P	L	I	T	L	P	T	K	Y	V	P	P	I	K	D	H	E	S	F	I	N
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		W	A	L	S	F	G	I	L	P	C	A	F	A	I	F	A	Y	L	I	S	G	A	L	D	L	H	N	N	A	A	K	L	L	R	V	R	Y	L	W	D	K	H	L	I	I	K	P	L	S	R	R	A	G	V	N	R	K	L	N	K
Secondary structure
SS confidence
Disorder																																																					?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	E	A	H	N	V	M	S	N	L	Y	Y	P	E	V	R	K	I	E	D	K	H	Y	I	E	L	F	W	N	K	V	Y	Y	F	W	I	F	F	E	F	S	I	I	A	L	I	S	F	L	I	I	F	F	C	K	Q	M	D	I	F
Secondary structure
SS confidence
Disorder		?	?	?																	?																																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.
Sequence		H	V	E	G	S	L	L	S	L	F	F	F	V	I	L	S	F	S	V	S	G	I	I	F	A	L	T	V	K	P	R	T	E	S	Q	V	G	K	I	P	D	D	K	I	K	E	F	F	T	K	N	N	I	N
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 1qgi chain A Region: 107 - 149 Aligned: 43 Modelled: 43 Confidence: 47.0% Identity: 14% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: Chitosanase Phyre2 PDB 1eys chain H domain 2 Region: 142 - 167 Aligned: 26 Modelled: 26 Confidence: 38.3% Identity: 38% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 3ckc chain A domain 1 Region: 7 - 64 Aligned: 58 Modelled: 58 Confidence: 31.3% Identity: 17% Fold: alpha-alpha superhelix Superfamily: TPR-like Family: SusD-like Phyre2 PDB 3pr3 chain B Region: 64 - 99 Aligned: 36 Modelled: 36 Confidence: 26.7% Identity: 33% PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of plasmodium falciparum glucose-6-phosphate2 isomerase (pf14_0341) in complex with fructose-6-phosphate Phyre2 PDB 1sqw chain A Region: 116 - 153 Aligned: 38 Modelled: 38 Confidence: 16.4% Identity: 21% PDB header:unknown function Chain: A: PDB Molecule:saccharomyces cerevisiae nip7p homolog; PDBTitle: crystal structure of kd93, a novel protein expressed in the2 human pro Phyre2 PDB 2ajt chain A domain 1 Region: 145 - 153 Aligned: 9 Modelled: 9 Confidence: 16.0% Identity: 67% Fold: Reductase/isomerase/elongation factor common domain Superfamily: FucI/AraA C-terminal domain-like Family: AraA C-terminal domain-like Phyre2 PDB 1w8j chain D Region: 37 - 130 Aligned: 94 Modelled: 94 Confidence: 15.8% Identity: 18% PDB header:motor protein Chain: D: PDB Molecule:myosin va; PDBTitle: crystal structure of myosin v motor domain -2 nucleotide-free Phyre2 PDB 1oed chain A Region: 49 - 121 Aligned: 73 Modelled: 73 Confidence: 15.4% Identity: 14% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 1lkx chain A Region: 49 - 130 Aligned: 78 Modelled: 82 Confidence: 13.2% Identity: 21% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Motor proteins Phyre2 PDB 2h8p chain C domain 1 Region: 181 - 222 Aligned: 41 Modelled: 42 Confidence: 12.8% Identity: 15% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 1mnd chain A domain 2 Region: 38 - 135 Aligned: 94 Modelled: 98 Confidence: 12.6% Identity: 20% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Motor proteins Phyre2 PDB 1eys chain H Region: 142 - 167 Aligned: 26 Modelled: 26 Confidence: 12.0% Identity: 38% PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum Phyre2 PDB 1br2 chain C Region: 45 - 131 Aligned: 83 Modelled: 87 Confidence: 10.8% Identity: 13% PDB header:muscle protein Chain: C: PDB Molecule:myosin; PDBTitle: smooth muscle myosin motor domain complexed with mgadp.alf4 Phyre2 PDB 2b0j chain A domain 1 Region: 72 - 117 Aligned: 46 Modelled: 46 Confidence: 10.5% Identity: 15% Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like Family: HMD dimerization domain-like Phyre2 PDB 1kx5 chain B Region: 105 - 153 Aligned: 39 Modelled: 49 Confidence: 9.8% Identity: 36% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 1nh1 chain A Region: 45 - 92 Aligned: 48 Modelled: 48 Confidence: 9.3% Identity: 29% Fold: Antivirulence factor Superfamily: Antivirulence factor Family: Antivirulence factor Phyre2 PDB 1nh1 chain A Region: 45 - 92 Aligned: 48 Modelled: 48 Confidence: 9.3% Identity: 29% PDB header:avirulence protein Chain: A: PDB Molecule:avirulence b protein; PDBTitle: crystal structure of the type iii effector avrb from2 pseudomonas syringae. Phyre2 PDB 3ujh chain B Region: 64 - 99 Aligned: 36 Modelled: 36 Confidence: 8.7% Identity: 31% PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of substrate-bound glucose-6-phosphate isomerase2 from toxoplasma gondii Phyre2 PDB 2zw3 chain B Region: 185 - 225 Aligned: 41 Modelled: 41 Confidence: 8.4% Identity: 20% PDB header:cell adhesion Chain: B: PDB Molecule:gap junction beta-2 protein; PDBTitle: structure of the connexin-26 gap junction channel at 3.52 angstrom resolution Phyre2 PDB 2rnd chain A Region: 109 - 131 Aligned: 23 Modelled: 23 Confidence: 7.8% Identity: 22% PDB header:endocytosis Chain: A: PDB Molecule:myc box-dependent-interacting protein 1; PDBTitle: structure of the n-terminal barpeptide in dpc micelles Phyre2 1 d1qgia_ 2 d1eysh2 3 d3ckca1 4 c3pr3B_ 5 c1sqwA_ 6 d2ajta1 7 c1w8jD_ 8 d1oeda_ 9 d1lkxa_ 10 d2h8pc1 11 d1mnda2 12 c1eysH_ 13 c1br2C_ 14 d2b0ja1 15 d1kx5b_ 16 d1nh1a_ 17 c1nh1A_ 18 c3ujhB_ 19 c2zw3B_ 20 c2rndA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Detailed template information

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

1 d1qgia_ 47.0 14 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Chitosanase 2 d1eysh2 38.3 38 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 3 d3ckca1 31.3 17 Fold:alpha-alpha superhelix Superfamily:TPR-like Family:SusD-like 4 c3pr3B_ 26.7 33 PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of plasmodium falciparum glucose-6-phosphate2 isomerase (pf14_0341) in complex with fructose-6-phosphate 5 c1sqwA_ 16.4 21 PDB header:unknown function Chain: A: PDB Molecule:saccharomyces cerevisiae nip7p homolog; PDBTitle: crystal structure of kd93, a novel protein expressed in the2 human pro 6 d2ajta1 16.0 67 Fold:Reductase/isomerase/elongation factor common domain Superfamily:FucI/AraA C-terminal domain-like Family:AraA C-terminal domain-like 7 c1w8jD_ 15.8 18 PDB header:motor protein Chain: D: PDB Molecule:myosin va; PDBTitle: crystal structure of myosin v motor domain -2 nucleotide-free 8 d1oeda_ 15.4 14 Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore 9 d1lkxa_ 13.2 21 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Motor proteins 10 d2h8pc1 12.8 15 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 11 d1mnda2 12.6 20 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Motor proteins 12 c1eysH_ 12.0 38 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 13 c1br2C_ 10.8 13 PDB header:muscle protein Chain: C: PDB Molecule:myosin; PDBTitle: smooth muscle myosin motor domain complexed with mgadp.alf4 14 d2b0ja1 10.5 15 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:HMD dimerization domain-like 15 d1kx5b_ 9.8 36 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 16 d1nh1a_ 9.3 29 Fold:Antivirulence factor Superfamily:Antivirulence factor Family:Antivirulence factor 17 c1nh1A_ 9.3 29 PDB header:avirulence protein Chain: A: PDB Molecule:avirulence b protein; PDBTitle: crystal structure of the type iii effector avrb from2 pseudomonas syringae. 18 c3ujhB_ 8.7 31 PDB header:isomerase Chain: B: PDB Molecule:glucose-6-phosphate isomerase; PDBTitle: crystal structure of substrate-bound glucose-6-phosphate isomerase2 from toxoplasma gondii 19 c2zw3B_ 8.4 20 PDB header:cell adhesion Chain: B: PDB Molecule:gap junction beta-2 protein; PDBTitle: structure of the connexin-26 gap junction channel at 3.52 angstrom resolution 20 c2rndA_ 7.8 22 PDB header:endocytosis Chain: A: PDB Molecule:myc box-dependent-interacting protein 1; PDBTitle: structure of the n-terminal barpeptide in dpc micelles 21 c2erpA_ not modelled 7.7 22 PDB header:toxin Chain: A: PDB Molecule:vascular apoptosis-inducing protein 1; PDBTitle: crystal structure of vascular apoptosis-inducing protein-1(inhibitor-2 bound form) 22 c3lhnB_ not modelled 7.4 83 PDB header:lipid binding protein Chain: B: PDB Molecule:lipoprotein; PDBTitle: crystal structure of putative lipoprotein (np_718719.1) from2 shewanella oneidensis at 1.42 a resolution 23 d2foka1 not modelled 7.4 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Restriction endonuclease FokI, N-terminal (recognition) domain 24 d1u1ia2 not modelled 7.2 25 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 25 c2kjyA_ not modelled 7.1 45 PDB header:signaling protein Chain: A: PDB Molecule:protein phosphatase 1 regulatory subunit 12a; PDBTitle: mypt1(658-714) 26 c2fcgF_ not modelled 6.9 50 PDB header:antimicrobial protein Chain: F: PDB Molecule:antibacterial protein fall-39, core peptide; PDBTitle: solution structure of the c-terminal fragment of human ll-37 27 d1khda1 not modelled 6.3 12 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 28 c1w9iA_ not modelled 6.2 21 PDB header:myosin Chain: A: PDB Molecule:myosin ii heavy chain; PDBTitle: myosin ii dictyostelium discoideum motor domain s456y bound2 with mgadp-befx 29 c1k6nH_ not modelled 6.2 47 PDB header:photosynthesis Chain: H: PDB Molecule:photosynthetic reaction center h subunit; PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides 30 c1g8xB_ not modelled 6.0 18 PDB header:structural protein Chain: B: PDB Molecule:myosin ii heavy chain fused to alpha-actinin 3; PDBTitle: structure of a genetically engineered molecular motor 31 d1cfea_ not modelled 5.9 38 Fold:PR-1-like Superfamily:PR-1-like Family:PR-1-like 32 d1d0xa2 not modelled 5.8 18 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Motor proteins 33 d1vjpa2 not modelled 5.7 40 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 34 d1rzhh2 not modelled 5.7 41 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 35 c2vb6A_ not modelled 5.3 24 PDB header:motor protein Chain: A: PDB Molecule:myosin vi; PDBTitle: myosin vi (md-insert2-cam, delta insert1) post-rigor state (2 crystal form 2)

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