Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	M	P	A	T	S	T	K	T	T	K	L	A	T	S	L	I	D	E	Y	A	L	L	G	W	R	A	M	L	T	E	V	N	L	S	P	K	P	G	L	V	D	R	I	N	C	G	A	H	K	D	M	A	L	E	D	F	H	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	A	L	A	I	Q	G	W	L	P	R	F	I	E	F	G	A	C	S	A	E	M	A	P	E	A	V	L	H	G	L	R	P	I	G	M	A	C	E	G	D	M	F	R	A	T	A	G	V	N	T	H	K	G	S	I	F	S	L	G
Secondary structure
SS confidence
Disorder																			?				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	L	C	A	A	I	G	R	L	L	Q	L	N	Q	P	V	T	P	T	T	V	C	S	T	A	A	S	F	C	R	G	L	T	D	R	E	L	R	T	N	N	S	Q	L	T	A	G	Q	R	L	Y	Q	Q	L	G	L	T	G	A	R
Secondary structure
SS confidence
Disorder															?																										?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	E	A	E	A	G	Y	P	L	V	I	N	H	A	L	P	H	Y	L	T	L	L	D	Q	G	L	D	P	E	L	A	L	L	D	T	L	L	L	L	M	A	I	N	G	D	T	N	V	A	S	R	G	G	E	G	G	L	R	W	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.
Sequence		Q	R	E	A	Q	T	L	L	Q	K	G	G	I	R	T	P	A	D	L	D	Y	L	R	Q	F	D	R	E	C	I	E	R	N	L	S	P	G	G	S	A	D	L	L	I	L	T	W	F	L	A	Q	I
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 3h9p chain B Region: 56 - 292 Aligned: 205 Modelled: 221 Confidence: 100.0% Identity: 18% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative triphosphoribosyl-dephospho-coa synthase; PDBTitle: crystal structure of putative triphosphoribosyl-dephospho-coa synthase2 from archaeoglobus fulgidus Phyre2 PDB 2xc7 chain A Region: 228 - 279 Aligned: 40 Modelled: 52 Confidence: 28.5% Identity: 28% PDB header:rna binding protein Chain: A: PDB Molecule:phosphorylated adapter rna export protein; PDBTitle: solution structure of phax-rbd in complex with ssrna Phyre2 PDB 2w4s chain D Region: 228 - 279 Aligned: 40 Modelled: 52 Confidence: 24.6% Identity: 25% PDB header:structural protein Chain: D: PDB Molecule:ankyrin-repeat protein; PDBTitle: novel rna-binding domain in cryptosporidium parvum at 2.52 angstrom resolution Phyre2 PDB 1p58 chain F Region: 95 - 126 Aligned: 32 Modelled: 32 Confidence: 18.9% Identity: 22% PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction Phyre2 PDB 3c6a chain A Region: 29 - 72 Aligned: 36 Modelled: 44 Confidence: 16.5% Identity: 17% PDB header:viral protein Chain: A: PDB Molecule:terminase large subunit; PDBTitle: crystal structure of the rb49 gp17 nuclease domain Phyre2 PDB 3omd chain B Region: 231 - 287 Aligned: 48 Modelled: 57 Confidence: 15.7% Identity: 17% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of unknown function protein from leptospirillum2 rubarum Phyre2 PDB 2f05 chain A domain 1 Region: 188 - 269 Aligned: 74 Modelled: 82 Confidence: 12.5% Identity: 12% Fold: PAH2 domain Superfamily: PAH2 domain Family: PAH2 domain Phyre2 PDB 1w53 chain A Region: 238 - 276 Aligned: 39 Modelled: 39 Confidence: 10.6% Identity: 23% Fold: KaiA/RbsU domain Superfamily: KaiA/RbsU domain Family: Phosphoserine phosphatase RsbU, N-terminal domain Phyre2 PDB 1o22 chain A Region: 260 - 277 Aligned: 18 Modelled: 18 Confidence: 9.8% Identity: 22% Fold: Hypothetical protein TM0875 Superfamily: Hypothetical protein TM0875 Family: Hypothetical protein TM0875 Phyre2 PDB 1q3q chain A domain 3 Region: 5 - 31 Aligned: 27 Modelled: 27 Confidence: 8.6% Identity: 30% Fold: GroEL-intermediate domain like Superfamily: GroEL-intermediate domain like Family: Group II chaperonin (CCT, TRIC), intermediate domain Phyre2 PDB 1au7 chain A domain 2 Region: 258 - 277 Aligned: 20 Modelled: 20 Confidence: 7.6% Identity: 30% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: POU-specific domain Phyre2 PDB 1a6d chain B domain 3 Region: 5 - 31 Aligned: 27 Modelled: 27 Confidence: 7.3% Identity: 22% Fold: GroEL-intermediate domain like Superfamily: GroEL-intermediate domain like Family: Group II chaperonin (CCT, TRIC), intermediate domain Phyre2 PDB 1a6d chain A domain 3 Region: 5 - 31 Aligned: 27 Modelled: 27 Confidence: 6.8% Identity: 22% Fold: GroEL-intermediate domain like Superfamily: GroEL-intermediate domain like Family: Group II chaperonin (CCT, TRIC), intermediate domain Phyre2 PDB 1s5q chain B Region: 188 - 269 Aligned: 74 Modelled: 82 Confidence: 6.2% Identity: 12% Fold: PAH2 domain Superfamily: PAH2 domain Family: PAH2 domain Phyre2 PDB 2l9v chain A Region: 260 - 279 Aligned: 20 Modelled: 20 Confidence: 6.1% Identity: 15% PDB header:rna binding protein Chain: A: PDB Molecule:pre-mrna-processing factor 40 homolog a; PDBTitle: nmr structure of the ff domain l24a mutant's folding transition state Phyre2 PDB 1uou chain A domain 2 Region: 237 - 282 Aligned: 38 Modelled: 46 Confidence: 5.2% Identity: 24% Fold: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain Superfamily: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain Family: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain Phyre2 1 c3h9pB_ 2 c2xc7A_ 3 c2w4sD_ 4 c1p58F_ 5 c3c6aA_ 6 c3omdB_ 7 d2f05a1 8 d1w53a_ 9 d1o22a_ 10 d1q3qa3 11 d1au7a2 12 d1a6db3 13 d1a6da3 14 d1s5qb_ 15 c2l9vA_ 16 d1uoua2

Detailed template information

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

1 c3h9pB_ 100.0 18 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative triphosphoribosyl-dephospho-coa synthase; PDBTitle: crystal structure of putative triphosphoribosyl-dephospho-coa synthase2 from archaeoglobus fulgidus 2 c2xc7A_ 28.5 28 PDB header:rna binding protein Chain: A: PDB Molecule:phosphorylated adapter rna export protein; PDBTitle: solution structure of phax-rbd in complex with ssrna 3 c2w4sD_ 24.6 25 PDB header:structural protein Chain: D: PDB Molecule:ankyrin-repeat protein; PDBTitle: novel rna-binding domain in cryptosporidium parvum at 2.52 angstrom resolution 4 c1p58F_ 18.9 22 PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 5 c3c6aA_ 16.5 17 PDB header:viral protein Chain: A: PDB Molecule:terminase large subunit; PDBTitle: crystal structure of the rb49 gp17 nuclease domain 6 c3omdB_ 15.7 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of unknown function protein from leptospirillum2 rubarum 7 d2f05a1 12.5 12 Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain 8 d1w53a_ 10.6 23 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Phosphoserine phosphatase RsbU, N-terminal domain 9 d1o22a_ 9.8 22 Fold:Hypothetical protein TM0875 Superfamily:Hypothetical protein TM0875 Family:Hypothetical protein TM0875 10 d1q3qa3 8.6 30 Fold:GroEL-intermediate domain like Superfamily:GroEL-intermediate domain like Family:Group II chaperonin (CCT, TRIC), intermediate domain 11 d1au7a2 7.6 30 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 12 d1a6db3 7.3 22 Fold:GroEL-intermediate domain like Superfamily:GroEL-intermediate domain like Family:Group II chaperonin (CCT, TRIC), intermediate domain 13 d1a6da3 6.8 22 Fold:GroEL-intermediate domain like Superfamily:GroEL-intermediate domain like Family:Group II chaperonin (CCT, TRIC), intermediate domain 14 d1s5qb_ 6.2 12 Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain 15 c2l9vA_ 6.1 15 PDB header:rna binding protein Chain: A: PDB Molecule:pre-mrna-processing factor 40 homolog a; PDBTitle: nmr structure of the ff domain l24a mutant's folding transition state 16 d1uoua2 5.2 24 Fold:Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain Family:Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

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