Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	K	E	Q	S	A	D	D	P	S	V	D	L	I	R	V	K	N	M	L	N	S	T	I	S	M	S	Y	P	D	V	V	I	A	C	I	E	H	K	V	S	L	E	A	F	R	A	I	E	A	A	L	V	K	H	D	N	N	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?							?			?	?	?																																	?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		K	D	Y	S	L	V	V	D
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 2isy chain A domain 2 Region: 35 - 53 Aligned: 19 Modelled: 19 Confidence: 10.9% Identity: 32% Fold: Iron-dependent repressor protein, dimerization domain Superfamily: Iron-dependent repressor protein, dimerization domain Family: Iron-dependent repressor protein, dimerization domain Phyre2 PDB 2ha9 chain A domain 1 Region: 24 - 55 Aligned: 31 Modelled: 32 Confidence: 7.7% Identity: 23% Fold: PFL-like glycyl radical enzymes Superfamily: PFL-like glycyl radical enzymes Family: SP0239-like Phyre2 PDB 1h3g chain A domain 1 Region: 14 - 39 Aligned: 26 Modelled: 25 Confidence: 7.3% Identity: 12% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: E-set domains of sugar-utilizing enzymes Phyre2 PDB 2p87 chain A Region: 54 - 68 Aligned: 14 Modelled: 15 Confidence: 7.2% Identity: 14% PDB header:splicing Chain: A: PDB Molecule:pre-mrna-splicing factor prp8; PDBTitle: crystal structure of the c-terminal domain of c. elegans2 pre-mrna splicing factor prp8 Phyre2 PDB 1xb4 chain A domain 1 Region: 21 - 58 Aligned: 38 Modelled: 38 Confidence: 6.5% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Vacuolar sorting protein domain Phyre2 PDB 1iow chain A domain 1 Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 5.6% Identity: 39% Fold: PreATP-grasp domain Superfamily: PreATP-grasp domain Family: D-Alanine ligase N-terminal domain Phyre2 PDB 3gpq chain A Region: 31 - 50 Aligned: 20 Modelled: 20 Confidence: 5.2% Identity: 35% PDB header:viral protein/rna Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: crystal structure of macro domain of chikungunya virus in complex with2 rna Phyre2 PDB 3cuq chain D Region: 37 - 58 Aligned: 22 Modelled: 22 Confidence: 5.2% Identity: 23% PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex Phyre2 1 d2isya2 2 d2ha9a1 3 d1h3ga1 4 c2p87A_ 5 d1xb4a1 6 d1iowa1 7 c3gpqA_ 8 c3cuqD_

Detailed template information

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

1 d2isya2 10.9 32 Fold:Iron-dependent repressor protein, dimerization domain Superfamily:Iron-dependent repressor protein, dimerization domain Family:Iron-dependent repressor protein, dimerization domain 2 d2ha9a1 7.7 23 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:SP0239-like 3 d1h3ga1 7.3 12 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:E-set domains of sugar-utilizing enzymes 4 c2p87A_ 7.2 14 PDB header:splicing Chain: A: PDB Molecule:pre-mrna-splicing factor prp8; PDBTitle: crystal structure of the c-terminal domain of c. elegans2 pre-mrna splicing factor prp8 5 d1xb4a1 6.5 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain 6 d1iowa1 5.6 39 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:D-Alanine ligase N-terminal domain 7 c3gpqA_ 5.2 35 PDB header:viral protein/rna Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: crystal structure of macro domain of chikungunya virus in complex with2 rna 8 c3cuqD_ 5.2 23 PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex

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

---

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