Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	A	A	L	F	G	C	Q	P	Y	L	V	Q	R	L	L	A	V	D	N	D	F	A	A	I	L	K	G	N	G	Q	Y	A	A	V	D	F	A	V	D	I	A	V	A	I	P	V	V	Q	A	F	F	N	G	Q	P	E	L	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	Q	A	M	K	F	T	V	V	H	C	C	I	L	F	L	S	D	G	G	S	I	A	A	W	G	Q	G	F	K	V	C	T	S	A	A	A	F	R	H	D	S	S	V	T	G	I	M	M	S	L	C	S	E	R	F	V	S	S	L
Secondary structure
SS confidence
Disorder																									?														?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.
Sequence		G	R	S	Y	T	T	S	F	P	V	S	G	K	H	Y	D	Q	V	Y	R	A	S	I	L	T	L	T	E	L	K	K	T	T	N	K	P	H	C	D	S	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 2gu0 chain A Region: 8 - 94 Aligned: 67 Modelled: 67 Confidence: 41.6% Identity: 24% PDB header:viral protein Chain: A: PDB Molecule:nonstructural protein 2; PDBTitle: crystal structure of human rotavirus nsp2 (group c /2 bristol strain) Phyre2 PDB 1s5q chain B Region: 2 - 66 Aligned: 62 Modelled: 65 Confidence: 29.9% Identity: 21% Fold: PAH2 domain Superfamily: PAH2 domain Family: PAH2 domain Phyre2 PDB 2f05 chain A domain 1 Region: 2 - 66 Aligned: 62 Modelled: 62 Confidence: 21.1% Identity: 19% Fold: PAH2 domain Superfamily: PAH2 domain Family: PAH2 domain Phyre2 PDB 1vp8 chain A Region: 85 - 92 Aligned: 8 Modelled: 8 Confidence: 18.7% Identity: 63% Fold: Pyruvate kinase C-terminal domain-like Superfamily: PK C-terminal domain-like Family: MTH1675-like Phyre2 PDB 1t57 chain A Region: 85 - 92 Aligned: 8 Modelled: 8 Confidence: 17.8% Identity: 75% Fold: Pyruvate kinase C-terminal domain-like Superfamily: PK C-terminal domain-like Family: MTH1675-like Phyre2 PDB 3bl2 chain A domain 1 Region: 133 - 141 Aligned: 9 Modelled: 9 Confidence: 16.0% Identity: 78% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 2rmr chain A Region: 2 - 61 Aligned: 48 Modelled: 60 Confidence: 13.4% Identity: 33% PDB header:transcription Chain: A: PDB Molecule:paired amphipathic helix protein sin3a; PDBTitle: solution structure of msin3a pah1 domain Phyre2 PDB 1utr chain A Region: 48 - 65 Aligned: 18 Modelled: 18 Confidence: 12.5% Identity: 28% Fold: Uteroglobin-like Superfamily: Uteroglobin-like Family: Uteroglobin-like Phyre2 PDB 1ccd chain A Region: 48 - 65 Aligned: 18 Modelled: 18 Confidence: 12.3% Identity: 28% Fold: Uteroglobin-like Superfamily: Uteroglobin-like Family: Uteroglobin-like Phyre2 PDB 1utg chain A Region: 48 - 65 Aligned: 18 Modelled: 18 Confidence: 9.5% Identity: 22% Fold: Uteroglobin-like Superfamily: Uteroglobin-like Family: Uteroglobin-like Phyre2 PDB 1n93 chain X Region: 53 - 95 Aligned: 38 Modelled: 43 Confidence: 9.0% Identity: 29% Fold: P40 nucleoprotein Superfamily: P40 nucleoprotein Family: P40 nucleoprotein Phyre2 PDB 1n93 chain X Region: 53 - 95 Aligned: 38 Modelled: 43 Confidence: 9.0% Identity: 29% PDB header:viral protein Chain: X: PDB Molecule:p40 nucleoprotein; PDBTitle: crystal structure of the borna disease virus nucleoprotein Phyre2 PDB 3qk9 chain B Region: 12 - 62 Aligned: 50 Modelled: 51 Confidence: 7.4% Identity: 14% PDB header:protein transport Chain: B: PDB Molecule:mitochondrial import inner membrane translocase subunit PDBTitle: yeast tim44 c-terminal domain complexed with cymal-3 Phyre2 PDB 2fhd chain A Region: 51 - 57 Aligned: 7 Modelled: 7 Confidence: 6.8% Identity: 71% PDB header:cell cycle Chain: A: PDB Molecule:dna repair protein rhp9/crb2; PDBTitle: crystal structure of crb2 tandem tudor domains Phyre2 PDB 3bd0 chain D Region: 17 - 57 Aligned: 41 Modelled: 41 Confidence: 6.6% Identity: 20% PDB header:peptide binding protein Chain: D: PDB Molecule:protein memo1; PDBTitle: crystal structure of memo, form ii Phyre2 PDB 1mb4 chain A domain 1 Region: 70 - 104 Aligned: 35 Modelled: 35 Confidence: 6.2% Identity: 26% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain Phyre2 PDB 1s28 chain A Region: 114 - 140 Aligned: 27 Modelled: 27 Confidence: 6.1% Identity: 26% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Type III secretory system chaperone Phyre2 PDB 1nlx chain A Region: 116 - 148 Aligned: 33 Modelled: 33 Confidence: 5.3% Identity: 21% Fold: Four-helical up-and-down bundle Superfamily: Group V grass pollen allergen Family: Group V grass pollen allergen Phyre2 1 c2gu0A_ 2 d1s5qb_ 3 d2f05a1 4 d1vp8a_ 5 d1t57a_ 6 d3bl2a1 7 c2rmrA_ 8 d1utra_ 9 d1ccda_ 10 d1utga_ 11 d1n93x_ 12 c1n93X_ 13 c3qk9B_ 14 c2fhdA_ 15 c3bd0D_ 16 d1mb4a1 17 d1s28a_ 18 d1nlxa_

Detailed template information

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

1 c2gu0A_ 41.6 24 PDB header:viral protein Chain: A: PDB Molecule:nonstructural protein 2; PDBTitle: crystal structure of human rotavirus nsp2 (group c /2 bristol strain) 2 d1s5qb_ 29.9 21 Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain 3 d2f05a1 21.1 19 Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain 4 d1vp8a_ 18.7 63 Fold:Pyruvate kinase C-terminal domain-like Superfamily:PK C-terminal domain-like Family:MTH1675-like 5 d1t57a_ 17.8 75 Fold:Pyruvate kinase C-terminal domain-like Superfamily:PK C-terminal domain-like Family:MTH1675-like 6 d3bl2a1 16.0 78 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 7 c2rmrA_ 13.4 33 PDB header:transcription Chain: A: PDB Molecule:paired amphipathic helix protein sin3a; PDBTitle: solution structure of msin3a pah1 domain 8 d1utra_ 12.5 28 Fold:Uteroglobin-like Superfamily:Uteroglobin-like Family:Uteroglobin-like 9 d1ccda_ 12.3 28 Fold:Uteroglobin-like Superfamily:Uteroglobin-like Family:Uteroglobin-like 10 d1utga_ 9.5 22 Fold:Uteroglobin-like Superfamily:Uteroglobin-like Family:Uteroglobin-like 11 d1n93x_ 9.0 29 Fold:P40 nucleoprotein Superfamily:P40 nucleoprotein Family:P40 nucleoprotein 12 c1n93X_ 9.0 29 PDB header:viral protein Chain: X: PDB Molecule:p40 nucleoprotein; PDBTitle: crystal structure of the borna disease virus nucleoprotein 13 c3qk9B_ 7.4 14 PDB header:protein transport Chain: B: PDB Molecule:mitochondrial import inner membrane translocase subunit PDBTitle: yeast tim44 c-terminal domain complexed with cymal-3 14 c2fhdA_ 6.8 71 PDB header:cell cycle Chain: A: PDB Molecule:dna repair protein rhp9/crb2; PDBTitle: crystal structure of crb2 tandem tudor domains 15 c3bd0D_ 6.6 20 PDB header:peptide binding protein Chain: D: PDB Molecule:protein memo1; PDBTitle: crystal structure of memo, form ii 16 d1mb4a1 6.2 26 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 17 d1s28a_ 6.1 26 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 18 d1nlxa_ 5.3 21 Fold:Four-helical up-and-down bundle Superfamily:Group V grass pollen allergen Family:Group V grass pollen allergen

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