Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	T	F	T	N	K	E	L	I	K	E	I	K	E	R	I	S	S	L	E	V	R	D	D	I	E	R	R	A	Y	E	I	A	L	V	S	L	E	V	E	P	D	E	R	E	A	Y	E	L	F	M	E	K	R	F	G	D	L	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?														?	?	?																?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.
Sequence		D	R	R	R	A	K	N	G	D	N	E	Y	M	A	W	D	M	T	L	G	W	I	I	W	Q	Q	R	A	G	I	H	F	S	T	M	S	Q	Q	E	V	K
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 2knu chain A Region: 70 - 81 Aligned: 12 Modelled: 12 Confidence: 47.3% Identity: 50% PDB header:membrane protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: solution structure of the transmembrane proximal region of2 the hepatis c virus e1 glycoprotein Phyre2 PDB 1lj2 chain B Region: 6 - 53 Aligned: 41 Modelled: 48 Confidence: 32.4% Identity: 27% PDB header:viral protein/ translation Chain: B: PDB Molecule:nonstructural rna-binding protein 34; PDBTitle: recognition of eif4g by rotavirus nsp3 reveals a basis for2 mrna circularization Phyre2 PDB 2jtv chain A Region: 1 - 32 Aligned: 32 Modelled: 32 Confidence: 14.4% Identity: 25% PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384 Phyre2 PDB 2ekw chain C Region: 2 - 51 Aligned: 49 Modelled: 50 Confidence: 12.9% Identity: 22% PDB header:contractile protein Chain: C: PDB Molecule:myosin catalytic light chain lc-1, mantle muscle; PDBTitle: the crystal structure of squid myosin s1 in the presence of2 so4 2- Phyre2 PDB 1wwi chain A domain 1 Region: 36 - 74 Aligned: 39 Modelled: 39 Confidence: 12.9% Identity: 26% Fold: Histone-fold Superfamily: Histone-fold Family: Bacterial histone-fold protein Phyre2 PDB 1dip chain A Region: 7 - 29 Aligned: 23 Modelled: 23 Confidence: 11.0% Identity: 35% PDB header:acetylation Chain: A: PDB Molecule:delta-sleep-inducing peptide immunoreactive PDBTitle: the solution structure of porcine delta-sleep-inducing2 peptide immunoreactive peptide, nmr, 10 structures Phyre2 PDB 1r4v chain A Region: 36 - 74 Aligned: 39 Modelled: 39 Confidence: 9.5% Identity: 18% Fold: Histone-fold Superfamily: Histone-fold Family: Bacterial histone-fold protein Phyre2 PDB 1sl7 chain A Region: 2 - 59 Aligned: 58 Modelled: 58 Confidence: 9.0% Identity: 26% Fold: EF Hand-like Superfamily: EF-hand Family: Calmodulin-like Phyre2 PDB 1fxk chain A Region: 7 - 23 Aligned: 17 Modelled: 17 Confidence: 8.4% Identity: 35% Fold: Long alpha-hairpin Superfamily: Prefoldin Family: Prefoldin Phyre2 PDB 1sfu chain A Region: 3 - 34 Aligned: 30 Modelled: 32 Confidence: 8.0% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Z-DNA binding domain Phyre2 PDB 2fm9 chain A domain 1 Region: 22 - 34 Aligned: 13 Modelled: 13 Confidence: 7.6% Identity: 15% Fold: SipA N-terminal domain-like Superfamily: SipA N-terminal domain-like Family: SipA N-terminal domain-like Phyre2 PDB 1d1d chain A domain 2 Region: 3 - 42 Aligned: 39 Modelled: 40 Confidence: 6.6% Identity: 26% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 2gff chain B Region: 33 - 66 Aligned: 34 Modelled: 34 Confidence: 5.9% Identity: 12% PDB header:sugar binding protein Chain: B: PDB Molecule:lsrg protein; PDBTitle: crystal structure of yersinia pestis lsrg Phyre2 PDB 2ogd chain B Region: 5 - 63 Aligned: 59 Modelled: 59 Confidence: 5.9% Identity: 12% PDB header:transferase Chain: B: PDB Molecule:farnesyl pyrophosphate synthase; PDBTitle: t. brucei farnesyl diphosphate synthase complexed with bisphosphonate2 bph-527 Phyre2 PDB 1z8y chain F Region: 87 - 98 Aligned: 12 Modelled: 12 Confidence: 5.8% Identity: 50% PDB header:virus Chain: F: PDB Molecule:spike glycoprotein e1; PDBTitle: mapping the e2 glycoprotein of alphaviruses Phyre2 PDB 1rj9 chain A domain 1 Region: 12 - 47 Aligned: 33 Modelled: 36 Confidence: 5.7% Identity: 39% Fold: Four-helical up-and-down bundle Superfamily: Domain of the SRP/SRP receptor G-proteins Family: Domain of the SRP/SRP receptor G-proteins Phyre2 PDB 2v33 chain A domain 1 Region: 90 - 98 Aligned: 9 Modelled: 9 Confidence: 5.4% Identity: 56% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Class II viral fusion proteins C-terminal domain Phyre2 PDB 2gyc chain 3 domain 1 Region: 51 - 57 Aligned: 7 Modelled: 7 Confidence: 5.4% Identity: 57% Fold: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Phyre2 PDB 1uiy chain A Region: 9 - 55 Aligned: 45 Modelled: 47 Confidence: 5.3% Identity: 29% Fold: ClpP/crotonase Superfamily: ClpP/crotonase Family: Crotonase-like Phyre2 1 c2knuA_ 2 c1lj2B_ 3 c2jtvA_ 4 c2ekwC_ 5 d1wwia1 6 c1dipA_ 7 d1r4va_ 8 d1sl7a_ 9 d1fxka_ 10 d1sfua_ 11 d2fm9a1 12 d1d1da2 13 c2gffB_ 14 c2ogdB_ 15 c1z8yF_ 16 d1rj9a1 17 d2v33a1 18 d2gyc31 19 d1uiya_

Detailed template information

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

1 c2knuA_ 47.3 50 PDB header:membrane protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: solution structure of the transmembrane proximal region of2 the hepatis c virus e1 glycoprotein 2 c1lj2B_ 32.4 27 PDB header:viral protein/ translation Chain: B: PDB Molecule:nonstructural rna-binding protein 34; PDBTitle: recognition of eif4g by rotavirus nsp3 reveals a basis for2 mrna circularization 3 c2jtvA_ 14.4 25 PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384 4 c2ekwC_ 12.9 22 PDB header:contractile protein Chain: C: PDB Molecule:myosin catalytic light chain lc-1, mantle muscle; PDBTitle: the crystal structure of squid myosin s1 in the presence of2 so4 2- 5 d1wwia1 12.9 26 Fold:Histone-fold Superfamily:Histone-fold Family:Bacterial histone-fold protein 6 c1dipA_ 11.0 35 PDB header:acetylation Chain: A: PDB Molecule:delta-sleep-inducing peptide immunoreactive PDBTitle: the solution structure of porcine delta-sleep-inducing2 peptide immunoreactive peptide, nmr, 10 structures 7 d1r4va_ 9.5 18 Fold:Histone-fold Superfamily:Histone-fold Family:Bacterial histone-fold protein 8 d1sl7a_ 9.0 26 Fold:EF Hand-like Superfamily:EF-hand Family:Calmodulin-like 9 d1fxka_ 8.4 35 Fold:Long alpha-hairpin Superfamily:Prefoldin Family:Prefoldin 10 d1sfua_ 8.0 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain 11 d2fm9a1 7.6 15 Fold:SipA N-terminal domain-like Superfamily:SipA N-terminal domain-like Family:SipA N-terminal domain-like 12 d1d1da2 6.6 26 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 13 c2gffB_ 5.9 12 PDB header:sugar binding protein Chain: B: PDB Molecule:lsrg protein; PDBTitle: crystal structure of yersinia pestis lsrg 14 c2ogdB_ 5.9 12 PDB header:transferase Chain: B: PDB Molecule:farnesyl pyrophosphate synthase; PDBTitle: t. brucei farnesyl diphosphate synthase complexed with bisphosphonate2 bph-527 15 c1z8yF_ 5.8 50 PDB header:virus Chain: F: PDB Molecule:spike glycoprotein e1; PDBTitle: mapping the e2 glycoprotein of alphaviruses 16 d1rj9a1 5.7 39 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 17 d2v33a1 5.4 56 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 18 d2gyc31 5.4 57 Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain 19 d1uiya_ 5.3 29 Fold:ClpP/crotonase Superfamily:ClpP/crotonase Family:Crotonase-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