Email l.a.kelley@imperial.ac.uk Description O14464 Date Mon Jul 2 19:10:21 BST 2012 Unique Job ID d9990755ffd217d3

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c3bbo6_ Top template information PDB header:ribosome Chain: 6: PDB Molecule:ribosomal protein l36; PDBTitle: homology model for the spinach chloroplast 50s subunit fitted to 9.4a2 cryo-em map of the 70s chlororibosome Confidence and coverage Confidence: 99.9% Coverage: 41% 38 residues ( 41% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template. You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library. Warning: 56% of your sequence is predicted disordered. Disordered regions cannot be meaningfully predicted. 3D viewing Interactive 3D view in Jmol

Sequence analysis

Secondary structure and disorder prediction

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: 56 - 93 Aligned: 38 Modelled: 38 Confidence: 99.9% Identity: 66% PDB header:ribosome Chain: 6: PDB Molecule:ribosomal protein l36; PDBTitle: homology model for the spinach chloroplast 50s subunit fitted to 9.4a2 cryo-em map of the 70s chlororibosome Phyre2 PDB 2qao chain 4 Region: 56 - 93 Aligned: 38 Modelled: 38 Confidence: 99.8% Identity: 53% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l36; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with neomycin. this file3 contains the 50s subunit of the second 70s ribosome, with4 neomycin bound. the entire crystal structure contains two5 70s ribosomes and is described in remark 400. Phyre2 PDB 2qbk chain 4 Region: 56 - 93 Aligned: 38 Modelled: 38 Confidence: 99.8% Identity: 53% 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: 56 - 93 Aligned: 37 Modelled: 38 Confidence: 99.8% Identity: 62% Fold: Ribosomal protein L36 Superfamily: Ribosomal protein L36 Family: Ribosomal protein L36 Phyre2 PDB 2zjr chain 4 domain 1 Region: 56 - 93 Aligned: 37 Modelled: 38 Confidence: 99.8% Identity: 68% Fold: Ribosomal protein L36 Superfamily: Ribosomal protein L36 Family: Ribosomal protein L36 Phyre2 PDB 1j0t chain A Region: 60 - 85 Aligned: 26 Modelled: 26 Confidence: 50.3% Identity: 23% Fold: Crustacean CHH/MIH/GIH neurohormone Superfamily: Crustacean CHH/MIH/GIH neurohormone Family: Crustacean CHH/MIH/GIH neurohormone Phyre2 PDB 3blz chain A domain 1 Region: 71 - 88 Aligned: 18 Modelled: 18 Confidence: 20.0% Identity: 22% Fold: Cystatin-like Superfamily: NTF2-like Family: Sbal0622-like Phyre2 PDB 3duk chain D Region: 71 - 88 Aligned: 18 Modelled: 18 Confidence: 11.5% Identity: 28% PDB header:unknown function Chain: D: PDB Molecule:ntf2-like protein of unknown function; PDBTitle: crystal structure of a ntf2-like protein of unknown function2 (mfla_0564) from methylobacillus flagellatus kt at 2.200 a resolution Phyre2 PDB 2zsh chain B Region: 53 - 61 Aligned: 9 Modelled: 9 Confidence: 8.2% Identity: 56% PDB header:hormone receptor Chain: B: PDB Molecule:della protein gai; PDBTitle: structural basis of gibberellin(ga3)-induced della2 recognition by the gibberellin receptor Phyre2 PDB 1cz6 chain A Region: 66 - 86 Aligned: 21 Modelled: 21 Confidence: 7.8% Identity: 29% PDB header:toxin Chain: A: PDB Molecule:protein (androctonin); PDBTitle: solution structure of androctonin Phyre2 PDB 3ccj chain U Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 7.3% Identity: 21% PDB header:ribosome Chain: U: PDB Molecule:50s ribosomal protein l24e; PDBTitle: structure of anisomycin resistant 50s ribosomal subunit: 23s rrna2 mutation c2534u Phyre2 PDB 4a1d chain K Region: 63 - 70 Aligned: 8 Modelled: 8 Confidence: 7.1% Identity: 75% PDB header:ribosome Chain: K: PDB Molecule:ubiquitin-60s ribosomal protein l40; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of3 molecule 4. Phyre2 PDB 2zkr chain U Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 6.8% Identity: 21% PDB header:ribosomal protein/rna Chain: U: PDB Molecule:rna expansion segment es41; PDBTitle: structure of a mammalian ribosomal 60s subunit within an 80s complex2 obtained by docking homology models of the rna and proteins into an3 8.7 a cryo-em map Phyre2 PDB 1vqo chain U domain 1 Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 6.8% Identity: 21% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: Ribosomal protein L24e Phyre2 PDB 3hsb chain B Region: 53 - 83 Aligned: 31 Modelled: 31 Confidence: 6.5% Identity: 29% PDB header:rna binding protein/rna Chain: B: PDB Molecule:protein hfq; PDBTitle: crystal structure of ymah (hfq) from bacillus subtilis in complex with2 an rna aptamer Phyre2 PDB 1kq1 chain W Region: 53 - 83 Aligned: 31 Modelled: 31 Confidence: 6.0% Identity: 13% PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq Phyre2 PDB 4a1e chain T Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 5.9% Identity: 14% PDB header:ribosome Chain: T: PDB Molecule:rpl24; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 Phyre2 PDB 3izc chain Z Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 5.9% Identity: 14% PDB header:ribosome Chain: Z: PDB Molecule:60s ribosomal protein rpl24 (l24e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 1kq1 chain A Region: 53 - 83 Aligned: 31 Modelled: 31 Confidence: 5.8% Identity: 13% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Pleiotropic translational regulator Hfq Phyre2 PDB 3iz5 chain Z Region: 70 - 83 Aligned: 14 Modelled: 14 Confidence: 5.2% Identity: 14% PDB header:ribosome Chain: Z: PDB Molecule:60s ribosomal protein l24 (l24e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 1 c3bbo6_ 2 c2qao4_ 3 c2qbk4_ 4 d1dfea_ 5 d2zjr41 6 d1j0ta_ 7 d3blza1 8 c3dukD_ 9 c2zshB_ 10 c1cz6A_ 11 c3ccjU_ 12 c4a1dK_ 13 c2zkru_ 14 d1vqou1 15 c3hsbB_ 16 c1kq1W_ 17 c4a1eT_ 18 c3izcZ_ 19 d1kq1a_ 20 c3iz5Z_

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