Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	P	V	F	T	V	R	F	L	R	E	V	F	L	S	F	Y	R	T	A	C	A	A	V	L	Q	P	A	P	S	A	G	W	F	R	K	H	K	S	P	P	A	M	R	A	G	G	C	I	H	P	S	G	R	W	C	P	V	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																					?					?	?	?							?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.
Sequence		S	S	T	V	P	A	T	G	L	H	Q	H	H	S	D	P	T	H	V	I	W	T	Q	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 2a45 chain H Region: 46 - 58 Aligned: 13 Modelled: 13 Confidence: 28.2% Identity: 62% PDB header:hydrolase/hydrolase inhibitor Chain: H: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of the complex between thrombin and the central "e"2 region of fibrin Phyre2 PDB 1jy2 chain O Region: 46 - 58 Aligned: 13 Modelled: 13 Confidence: 26.0% Identity: 54% PDB header:blood clotting Chain: O: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of the central region of bovine2 fibrinogen (e5 fragment) at 1.4 angstroms resolution Phyre2 PDB 2cs3 chain A domain 1 Region: 44 - 65 Aligned: 22 Modelled: 22 Confidence: 23.6% Identity: 41% Fold: RING/U-box Superfamily: RING/U-box Family: Variant RING domain Phyre2 PDB 1pf5 chain A Region: 26 - 71 Aligned: 46 Modelled: 46 Confidence: 22.0% Identity: 22% Fold: Bacillus chorismate mutase-like Superfamily: YjgF-like Family: YjgF/L-PSP Phyre2 PDB 2fml chain A domain 1 Region: 3 - 25 Aligned: 23 Modelled: 23 Confidence: 17.2% Identity: 26% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Nudix-associated domain Phyre2 PDB 2axt chain F domain 1 Region: 3 - 10 Aligned: 8 Modelled: 8 Confidence: 16.2% Identity: 63% Fold: Single transmembrane helix Superfamily: Cytochrome b559 subunits Family: Cytochrome b559 subunits Phyre2 PDB 1w5c chain L Region: 3 - 10 Aligned: 8 Modelled: 8 Confidence: 16.1% Identity: 63% PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b559 beta subunit; PDBTitle: photosystem ii from thermosynechococcus elongatus Phyre2 PDB 1g26 chain A Region: 49 - 56 Aligned: 8 Modelled: 8 Confidence: 14.5% Identity: 63% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Granulin repeat Family: Granulin repeat Phyre2 PDB 1p8b chain A Region: 41 - 54 Aligned: 14 Modelled: 14 Confidence: 13.4% Identity: 43% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Albumin 1 Phyre2 PDB 1ju8 chain A Region: 41 - 54 Aligned: 14 Modelled: 14 Confidence: 12.2% Identity: 50% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Albumin 1 Phyre2 PDB 1khi chain A Region: 43 - 72 Aligned: 30 Modelled: 30 Confidence: 10.4% Identity: 40% PDB header:structural protein Chain: A: PDB Molecule:hex1; PDBTitle: crystal structure of hex1 Phyre2 PDB 3sc0 chain A Region: 46 - 57 Aligned: 12 Modelled: 12 Confidence: 10.1% Identity: 58% PDB header:oxidoreductase Chain: A: PDB Molecule:methylmalonic aciduria and homocystinuria type c protein; PDBTitle: crystal structure of mmachc (1-238), a human b12 processing enzyme,2 complexed with methylcobalamin Phyre2 PDB 1v33 chain A Region: 44 - 57 Aligned: 14 Modelled: 14 Confidence: 10.0% Identity: 21% Fold: Prim-pol domain Superfamily: Prim-pol domain Family: PriA-like Phyre2 PDB 1khi chain A domain 1 Region: 43 - 72 Aligned: 30 Modelled: 30 Confidence: 9.8% Identity: 33% Fold: SH3-like barrel Superfamily: Translation proteins SH3-like domain Family: eIF5a N-terminal domain-like Phyre2 PDB 1imt chain A domain 2 Region: 53 - 76 Aligned: 24 Modelled: 24 Confidence: 9.7% Identity: 42% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Colipase-like Family: Colipase-like Phyre2 PDB 2rp5 chain A Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 8.8% Identity: 60% PDB header:transcription Chain: A: PDB Molecule:putative uncharacterized protein cep-1; PDBTitle: solution structure of the oligomerization domain in cep-1 Phyre2 PDB 1eg3 chain A domain 1 Region: 15 - 22 Aligned: 8 Modelled: 8 Confidence: 8.7% Identity: 63% Fold: EF Hand-like Superfamily: EF-hand Family: EF-hand modules in multidomain proteins Phyre2 PDB 1y96 chain D Region: 9 - 22 Aligned: 14 Modelled: 14 Confidence: 7.9% Identity: 29% PDB header:rna binding protein Chain: D: PDB Molecule:gem-associated protein 7; PDBTitle: crystal structure of the gemin6/gemin7 heterodimer from the2 human smn complex Phyre2 PDB 1g71 chain A Region: 44 - 57 Aligned: 14 Modelled: 14 Confidence: 7.6% Identity: 21% Fold: Prim-pol domain Superfamily: Prim-pol domain Family: PriA-like Phyre2 PDB 3i5d chain C Region: 44 - 65 Aligned: 22 Modelled: 21 Confidence: 7.0% Identity: 36% PDB header:transport protein Chain: C: PDB Molecule:p2x purinoceptor; PDBTitle: crystal structure of the atp-gated p2x4 ion channel in the closed, apo2 state at 3.5 angstroms (r3) Phyre2 1 c2a45H_ 2 c1jy2O_ 3 d2cs3a1 4 d1pf5a_ 5 d2fmla1 6 d2axtf1 7 c1w5cL_ 8 d1g26a_ 9 d1p8ba_ 10 d1ju8a_ 11 c1khiA_ 12 c3sc0A_ 13 d1v33a_ 14 d1khia1 15 d1imta2 16 c2rp5A_ 17 d1eg3a1 18 c1y96D_ 19 d1g71a_ 20 c3i5dC_ 21 22 23 24 25 26

Detailed template information

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

1 c2a45H_ 28.2 62 PDB header:hydrolase/hydrolase inhibitor Chain: H: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of the complex between thrombin and the central "e"2 region of fibrin 2 c1jy2O_ 26.0 54 PDB header:blood clotting Chain: O: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of the central region of bovine2 fibrinogen (e5 fragment) at 1.4 angstroms resolution 3 d2cs3a1 23.6 41 Fold:RING/U-box Superfamily:RING/U-box Family:Variant RING domain 4 d1pf5a_ 22.0 22 Fold:Bacillus chorismate mutase-like Superfamily:YjgF-like Family:YjgF/L-PSP 5 d2fmla1 17.2 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Nudix-associated domain 6 d2axtf1 16.2 63 Fold:Single transmembrane helix Superfamily:Cytochrome b559 subunits Family:Cytochrome b559 subunits 7 c1w5cL_ 16.1 63 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b559 beta subunit; PDBTitle: photosystem ii from thermosynechococcus elongatus 8 d1g26a_ 14.5 63 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Granulin repeat Family:Granulin repeat 9 d1p8ba_ 13.4 43 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Albumin 1 10 d1ju8a_ 12.2 50 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Albumin 1 11 c1khiA_ 10.4 40 PDB header:structural protein Chain: A: PDB Molecule:hex1; PDBTitle: crystal structure of hex1 12 c3sc0A_ 10.1 58 PDB header:oxidoreductase Chain: A: PDB Molecule:methylmalonic aciduria and homocystinuria type c protein; PDBTitle: crystal structure of mmachc (1-238), a human b12 processing enzyme,2 complexed with methylcobalamin 13 d1v33a_ 10.0 21 Fold:Prim-pol domain Superfamily:Prim-pol domain Family:PriA-like 14 d1khia1 9.8 33 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:eIF5a N-terminal domain-like 15 d1imta2 9.7 42 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Colipase-like Family:Colipase-like 16 c2rp5A_ 8.8 60 PDB header:transcription Chain: A: PDB Molecule:putative uncharacterized protein cep-1; PDBTitle: solution structure of the oligomerization domain in cep-1 17 d1eg3a1 8.7 63 Fold:EF Hand-like Superfamily:EF-hand Family:EF-hand modules in multidomain proteins 18 c1y96D_ 7.9 29 PDB header:rna binding protein Chain: D: PDB Molecule:gem-associated protein 7; PDBTitle: crystal structure of the gemin6/gemin7 heterodimer from the2 human smn complex 19 d1g71a_ 7.6 21 Fold:Prim-pol domain Superfamily:Prim-pol domain Family:PriA-like 20 c3i5dC_ 7.0 36 PDB header:transport protein Chain: C: PDB Molecule:p2x purinoceptor; PDBTitle: crystal structure of the atp-gated p2x4 ion channel in the closed, apo2 state at 3.5 angstroms (r3) 21 d1twfb_ not modelled 7.0 27 Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase Family:RNA-polymerase beta 22 d1fasa_ not modelled 6.9 50 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Snake venom toxins 23 d1smpi_ not modelled 5.2 41 Fold:Streptavidin-like Superfamily:beta-Barrel protease inhibitors Family:Metalloprotease inhibitor 24 d1iz6a1 not modelled 5.1 23 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:eIF5a N-terminal domain-like 25 c2e2sA_ not modelled 5.1 41 PDB header:toxin Chain: A: PDB Molecule:agelenin; PDBTitle: solution structure of agelenin, an insecticidal peptide2 from the venom of agelena opulenta 26 d2eifa1 not modelled 5.0 20 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:eIF5a N-terminal domain-like

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