Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	S	L	S	R	P	R	V	E	F	I	S	T	I	L	Q	T	V	L	N	L	G	L	L	C	L	G	L	I	L	V	V	F	L	G	K	E	T	V	H	L	A	D	V	L	F	A	P	E	Q	T	S	K	Y	E	L	V	E	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																																											?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	V	V	Y	F	L	Y	F	E	F	I	A	L	I	V	K	Y	F	Q	S	G	F	H	F	P	L	R	Y	F	V	Y	I	G	I	T	A	I	V	R	L	I	I	V	D	H	K	S	P	L	D	V	L	I	Y	S	A	A	I	L	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.
Sequence		L	V	I	T	L	W	L	C	N	S	K	R	L	K	R	E
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 1si2 chain A Region: 74 - 89 Aligned: 16 Modelled: 16 Confidence: 12.3% Identity: 25% Fold: SH3-like barrel Superfamily: PAZ domain Family: PAZ domain Phyre2 PDB 1t2s chain A Region: 74 - 89 Aligned: 15 Modelled: 16 Confidence: 9.6% Identity: 40% Fold: SH3-like barrel Superfamily: PAZ domain Family: PAZ domain Phyre2 PDB 1r6z chain A Region: 74 - 89 Aligned: 15 Modelled: 16 Confidence: 9.5% Identity: 40% PDB header:gene regulation Chain: A: PDB Molecule:chimera of maltose-binding periplasmic protein and PDBTitle: the crystal structure of the argonaute2 paz domain (as a mbp fusion) Phyre2 PDB 1r6z chain A domain 1 Region: 74 - 89 Aligned: 15 Modelled: 16 Confidence: 8.7% Identity: 40% Fold: SH3-like barrel Superfamily: PAZ domain Family: PAZ domain Phyre2 PDB 1m56 chain D Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 7.6% Identity: 6% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1fc3 chain A Region: 69 - 83 Aligned: 15 Modelled: 15 Confidence: 7.5% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: Spo0A Phyre2 1 d1si2a_ 2 d1t2sa_ 3 c1r6zA_ 4 d1r6za1 5 d1m56d_ 6 d1fc3a_

Detailed template information

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

1 d1si2a_ 12.3 25 Fold:SH3-like barrel Superfamily:PAZ domain Family:PAZ domain 2 d1t2sa_ 9.6 40 Fold:SH3-like barrel Superfamily:PAZ domain Family:PAZ domain 3 c1r6zA_ 9.5 40 PDB header:gene regulation Chain: A: PDB Molecule:chimera of maltose-binding periplasmic protein and PDBTitle: the crystal structure of the argonaute2 paz domain (as a mbp fusion) 4 d1r6za1 8.7 40 Fold:SH3-like barrel Superfamily:PAZ domain Family:PAZ domain 5 d1m56d_ 7.6 6 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 6 d1fc3a_ 7.5 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:Spo0A

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