Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	Q	R	I	T	V	T	V	D	S	D	S	Y	Q	L	L	K	A	Y	D	V	N	I	S	G	L	V	S	T	T	M	Q	N	E	A	R	R	L	R	A	E	R	W	K	A	E	N	Q	E	G	M	A	E	V	A	R	F	I	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.
Sequence		M	N	G	S	F	A	D	E	N	R	D	W
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 2adl chain B Region: 1 - 72 Aligned: 72 Modelled: 72 Confidence: 100.0% Identity: 96% PDB header:dna binding protein Chain: B: PDB Molecule:ccda; PDBTitle: solution structure of the bacterial antitoxin ccda:2 implications for dna and toxin binding Phyre2 PDB 3g7z chain D Region: 40 - 72 Aligned: 33 Modelled: 33 Confidence: 99.8% Identity: 100% PDB header:toxin/toxin repressor Chain: D: PDB Molecule:protein ccda; PDBTitle: ccdb dimer in complex with two c-terminal ccda domains Phyre2 PDB 2xzm chain V Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 23.1% Identity: 44% PDB header:ribosome Chain: V: PDB Molecule:rps17e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 Phyre2 PDB 2zou chain B Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 12.6% Identity: 30% PDB header:cell adhesion Chain: B: PDB Molecule:spondin-1; PDBTitle: crystal struture of human f-spondin reeler domain (fragment 2) Phyre2 PDB 2db7 chain A domain 1 Region: 49 - 59 Aligned: 11 Modelled: 11 Confidence: 11.5% Identity: 55% Fold: Orange domain-like Superfamily: Orange domain-like Family: Hairy Orange domain Phyre2 PDB 3coo chain B Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 10.6% Identity: 30% PDB header:cell adhesion Chain: B: PDB Molecule:spondin-1; PDBTitle: the crystal structure of reelin-n domain of f-spondin Phyre2 PDB 1qk9 chain A Region: 52 - 72 Aligned: 21 Modelled: 21 Confidence: 9.5% Identity: 24% Fold: DNA-binding domain Superfamily: DNA-binding domain Family: Methyl-CpG-binding domain, MBD Phyre2 PDB 3d0w chain D Region: 33 - 59 Aligned: 27 Modelled: 27 Confidence: 6.6% Identity: 22% PDB header:structural genomics, unknown function Chain: D: PDB Molecule:yflh protein; PDBTitle: crystal structure of yflh protein from bacillus subtilis.2 northeast structural genomics consortium target sr326 Phyre2 PDB 2i3e chain A Region: 18 - 37 Aligned: 20 Modelled: 20 Confidence: 5.7% Identity: 30% PDB header:hydrolase Chain: A: PDB Molecule:g-rich; PDBTitle: solution structure of catalytic domain of goldfish rich2 protein Phyre2 PDB 1wz3 chain A domain 1 Region: 36 - 60 Aligned: 25 Modelled: 25 Confidence: 5.4% Identity: 24% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: APG12-like Phyre2 1 c2adlB_ 2 c3g7zD_ 3 c2xzmV_ 4 c2zouB_ 5 d2db7a1 6 c3cooB_ 7 d1qk9a_ 8 c3d0wD_ 9 c2i3eA_ 10 d1wz3a1

Detailed template information

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

1 c2adlB_ 100.0 96 PDB header:dna binding protein Chain: B: PDB Molecule:ccda; PDBTitle: solution structure of the bacterial antitoxin ccda:2 implications for dna and toxin binding 2 c3g7zD_ 99.8 100 PDB header:toxin/toxin repressor Chain: D: PDB Molecule:protein ccda; PDBTitle: ccdb dimer in complex with two c-terminal ccda domains 3 c2xzmV_ 23.1 44 PDB header:ribosome Chain: V: PDB Molecule:rps17e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 4 c2zouB_ 12.6 30 PDB header:cell adhesion Chain: B: PDB Molecule:spondin-1; PDBTitle: crystal struture of human f-spondin reeler domain (fragment 2) 5 d2db7a1 11.5 55 Fold:Orange domain-like Superfamily:Orange domain-like Family:Hairy Orange domain 6 c3cooB_ 10.6 30 PDB header:cell adhesion Chain: B: PDB Molecule:spondin-1; PDBTitle: the crystal structure of reelin-n domain of f-spondin 7 d1qk9a_ 9.5 24 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:Methyl-CpG-binding domain, MBD 8 c3d0wD_ 6.6 22 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:yflh protein; PDBTitle: crystal structure of yflh protein from bacillus subtilis.2 northeast structural genomics consortium target sr326 9 c2i3eA_ 5.7 30 PDB header:hydrolase Chain: A: PDB Molecule:g-rich; PDBTitle: solution structure of catalytic domain of goldfish rich2 protein 10 d1wz3a1 5.4 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:APG12-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

---

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