Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	L	F	W	A	M	L	S	F	I	T	R	L	P	V	P	R	R	W	S	Q	G	L	D	F	E	H	Y	S	R	G	I	I	T	F	P	L	I	G	L	L	L	G	A	I	S	G	L	V	F	M	V	L	Q	A	W	C	G
Secondary structure
SS confidence
Disorder		?	?																		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	P	L	A	A	L	F	S	V	L	V	L	V	L	M	T	G	G	F	H	L	D	G	L	A	D	T	C	D	G	V	F	S	A	R	S	R	D	R	M	L	E	I	M	R	D	S	R	L	G	T	H	G	G	L	A	L	I	F	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	L	A	K	I	L	V	L	S	E	L	A	L	R	G	E	S	I	L	A	S	L	A	A	A	C	A	V	S	R	G	T	A	A	L	L	M	Y	R	H	R	Y	A	R	E	E	G	L	G	N	V	F	I	G	K	I	D	G	R	Q
Secondary structure
SS confidence
Disorder																																										?	?	?		?			?						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		T	C	V	T	L	G	L	A	A	I	F	A	A	V	L	L	P	G	M	H	G	V	A	A	M	V	V	T	M	V	A	I	F	I	L	G	Q	L	L	K	R	T	L	G	G	Q	T	G	D	T	L	G	A	A	I	E	L	G	E	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.
Sequence		V	F	L	L	A	L	L
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 1m0f chain B Region: 216 - 229 Aligned: 14 Modelled: 14 Confidence: 31.1% Identity: 36% PDB header:virus Chain: B: PDB Molecule:scaffolding protein b; PDBTitle: structural studies of bacteriophage alpha3 assembly, cryo-2 electron microscopy Phyre2 PDB 1pvg chain A domain 1 Region: 77 - 86 Aligned: 10 Modelled: 10 Confidence: 16.1% Identity: 40% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: DNA gyrase/MutL, second domain Phyre2 PDB 2v1s chain D Region: 74 - 107 Aligned: 34 Modelled: 34 Confidence: 15.8% Identity: 12% PDB header:oxidoreductase Chain: D: PDB Molecule:mitochondrial import receptor subunit tom20 homolog; PDBTitle: crystal structure of rat tom20-aldh presequence complex Phyre2 PDB 2d6f chain C domain 1 Region: 96 - 106 Aligned: 11 Modelled: 11 Confidence: 14.5% Identity: 36% Fold: GatB/YqeY motif Superfamily: GatB/YqeY motif Family: GatB/GatE C-terminal domain-like Phyre2 PDB 1ckq chain A Region: 92 - 106 Aligned: 15 Modelled: 15 Confidence: 10.4% Identity: 33% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: Restriction endonuclease EcoRI Phyre2 PDB 1om2 chain A Region: 74 - 107 Aligned: 34 Modelled: 34 Confidence: 10.2% Identity: 12% Fold: Open three-helical up-and-down bundle Superfamily: Mitochondrial import receptor subunit Tom20 Family: Mitochondrial import receptor subunit Tom20 Phyre2 PDB 1kij chain A domain 1 Region: 77 - 86 Aligned: 10 Modelled: 10 Confidence: 9.9% Identity: 40% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: DNA gyrase/MutL, second domain Phyre2 PDB 1s16 chain A domain 1 Region: 77 - 86 Aligned: 10 Modelled: 10 Confidence: 9.7% Identity: 50% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: DNA gyrase/MutL, second domain Phyre2 PDB 1ei1 chain A domain 1 Region: 77 - 86 Aligned: 10 Modelled: 10 Confidence: 9.6% Identity: 50% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: DNA gyrase/MutL, second domain Phyre2 PDB 1otf chain A Region: 91 - 106 Aligned: 16 Modelled: 16 Confidence: 9.4% Identity: 13% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: 4-oxalocrotonate tautomerase-like Phyre2 PDB 1bjp chain A Region: 91 - 106 Aligned: 16 Modelled: 16 Confidence: 6.0% Identity: 19% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: 4-oxalocrotonate tautomerase-like Phyre2 1 c1m0fB_ 2 d1pvga1 3 c2v1sD_ 4 d2d6fc1 5 d1ckqa_ 6 d1om2a_ 7 d1kija1 8 d1s16a1 9 d1ei1a1 10 d1otfa_ 11 d1bjpa_

Detailed template information

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

1 c1m0fB_ 31.1 36 PDB header:virus Chain: B: PDB Molecule:scaffolding protein b; PDBTitle: structural studies of bacteriophage alpha3 assembly, cryo-2 electron microscopy 2 d1pvga1 16.1 40 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:DNA gyrase/MutL, second domain 3 c2v1sD_ 15.8 12 PDB header:oxidoreductase Chain: D: PDB Molecule:mitochondrial import receptor subunit tom20 homolog; PDBTitle: crystal structure of rat tom20-aldh presequence complex 4 d2d6fc1 14.5 36 Fold:GatB/YqeY motif Superfamily:GatB/YqeY motif Family:GatB/GatE C-terminal domain-like 5 d1ckqa_ 10.4 33 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease EcoRI 6 d1om2a_ 10.2 12 Fold:Open three-helical up-and-down bundle Superfamily:Mitochondrial import receptor subunit Tom20 Family:Mitochondrial import receptor subunit Tom20 7 d1kija1 9.9 40 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:DNA gyrase/MutL, second domain 8 d1s16a1 9.7 50 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:DNA gyrase/MutL, second domain 9 d1ei1a1 9.6 50 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:DNA gyrase/MutL, second domain 10 d1otfa_ 9.4 13 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like 11 d1bjpa_ 6.0 19 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-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