Secondary structure and disorder prediction

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Sequence		M	K	V	L	N	S	L	R	T	A	K	E	R	H	P	D	C	Q	I	V	K	R	K	G	R	L	Y	V	I	C	K	S	N	P	R	F	K	A	V	Q	G	R	K	K	K	R
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 3bbo chain 6 Region: 1 - 41 Aligned: 38 Modelled: 41 Confidence: 99.1% Identity: 55% PDB header:ribosome Chain: 6: PDB Molecule:ribosomal protein l36; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2qbk chain 4 Region: 1 - 41 Aligned: 38 Modelled: 41 Confidence: 98.8% Identity: 47% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l36; PDBTitle: crystal structure of the bacterial ribosome from escherichia2 coli in complex with gentamicin and ribosome recycling3 factor (rrf). this file contains the 50s subunit of the4 second 70s ribosome, with gentamicin and rrf bound. the5 entire crystal structure contains two 70s ribosomes and is6 described in remark 400. Phyre2 PDB 1dfe chain A Region: 1 - 41 Aligned: 37 Modelled: 41 Confidence: 98.7% Identity: 49% Fold: Ribosomal protein L36 Superfamily: Ribosomal protein L36 Family: Ribosomal protein L36 Phyre2 PDB 2zjr chain 4 domain 1 Region: 9 - 41 Aligned: 32 Modelled: 33 Confidence: 98.4% Identity: 44% Fold: Ribosomal protein L36 Superfamily: Ribosomal protein L36 Family: Ribosomal protein L36 Phyre2 PDB 1w7a chain B domain 4 Region: 9 - 27 Aligned: 19 Modelled: 19 Confidence: 16.2% Identity: 32% Fold: MutS N-terminal domain-like Superfamily: DNA repair protein MutS, domain I Family: DNA repair protein MutS, domain I Phyre2 PDB 1ni8 chain A Region: 2 - 19 Aligned: 18 Modelled: 18 Confidence: 13.3% Identity: 33% Fold: H-NS histone-like proteins Superfamily: H-NS histone-like proteins Family: H-NS histone-like proteins Phyre2 PDB 1cz6 chain A Region: 15 - 34 Aligned: 20 Modelled: 20 Confidence: 8.2% Identity: 30% PDB header:toxin Chain: A: PDB Molecule:protein (androctonin); PDBTitle: solution structure of androctonin Phyre2 PDB 1wb9 chain A domain 4 Region: 4 - 29 Aligned: 26 Modelled: 26 Confidence: 6.0% Identity: 23% Fold: MutS N-terminal domain-like Superfamily: DNA repair protein MutS, domain I Family: DNA repair protein MutS, domain I Phyre2 PDB 1l4d chain B Region: 15 - 31 Aligned: 17 Modelled: 17 Confidence: 5.9% Identity: 35% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 1ewq chain A domain 4 Region: 3 - 29 Aligned: 27 Modelled: 27 Confidence: 5.9% Identity: 19% Fold: MutS N-terminal domain-like Superfamily: DNA repair protein MutS, domain I Family: DNA repair protein MutS, domain I Phyre2 PDB 1ni5 chain A domain 4 Region: 13 - 30 Aligned: 18 Modelled: 18 Confidence: 5.7% Identity: 22% Fold: MesJ substrate recognition domain-like Superfamily: MesJ substrate recognition domain-like Family: MesJ substrate recognition domain-like Phyre2 PDB 1l4z chain B Region: 15 - 31 Aligned: 17 Modelled: 17 Confidence: 5.5% Identity: 35% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 1 c3bbo6_ 2 c2qbk4_ 3 d1dfea_ 4 d2zjr41 5 d1w7ab4 6 d1ni8a_ 7 c1cz6A_ 8 d1wb9a4 9 d1l4db_ 10 d1ewqa4 11 d1ni5a4 12 d1l4zb_

Detailed template information

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

1 c3bbo6_ 99.1 55 PDB header:ribosome Chain: 6: PDB Molecule:ribosomal protein l36; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 2 c2qbk4_ 98.8 47 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l36; PDBTitle: crystal structure of the bacterial ribosome from escherichia2 coli in complex with gentamicin and ribosome recycling3 factor (rrf). this file contains the 50s subunit of the4 second 70s ribosome, with gentamicin and rrf bound. the5 entire crystal structure contains two 70s ribosomes and is6 described in remark 400. 3 d1dfea_ 98.7 49 Fold:Ribosomal protein L36 Superfamily:Ribosomal protein L36 Family:Ribosomal protein L36 4 d2zjr41 98.4 44 Fold:Ribosomal protein L36 Superfamily:Ribosomal protein L36 Family:Ribosomal protein L36 5 d1w7ab4 16.2 32 Fold:MutS N-terminal domain-like Superfamily:DNA repair protein MutS, domain I Family:DNA repair protein MutS, domain I 6 d1ni8a_ 13.3 33 Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins 7 c1cz6A_ 8.2 30 PDB header:toxin Chain: A: PDB Molecule:protein (androctonin); PDBTitle: solution structure of androctonin 8 d1wb9a4 6.0 23 Fold:MutS N-terminal domain-like Superfamily:DNA repair protein MutS, domain I Family:DNA repair protein MutS, domain I 9 d1l4db_ 5.9 35 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 10 d1ewqa4 5.9 19 Fold:MutS N-terminal domain-like Superfamily:DNA repair protein MutS, domain I Family:DNA repair protein MutS, domain I 11 d1ni5a4 5.7 22 Fold:MesJ substrate recognition domain-like Superfamily:MesJ substrate recognition domain-like Family:MesJ substrate recognition domain-like 12 d1l4zb_ 5.5 35 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase

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