Email l.a.kelley@imperial.ac.uk Description O14455 Date Mon Jul 2 19:10:21 BST 2012 Unique Job ID 51cdeac384d4f765

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c4a19Q_ Top template information PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein l36; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 2. Confidence and coverage Confidence: 100.0% Coverage: 96% 96 residues ( 96% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template. 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 4a19 chain Q Region: 4 - 99 Aligned: 96 Modelled: 96 Confidence: 100.0% Identity: 38% PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein l36; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 2. Phyre2 PDB 3izc chain K Region: 24 - 100 Aligned: 77 Modelled: 77 Confidence: 100.0% Identity: 100% PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein rpl16 (l13p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 3iz5 chain K Region: 33 - 99 Aligned: 67 Modelled: 67 Confidence: 100.0% Identity: 46% PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l13a (l13p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 3b5m chain D Region: 41 - 62 Aligned: 20 Modelled: 22 Confidence: 11.3% Identity: 35% PDB header:structural genomics, unknown function Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of conserved uncharacterized protein from2 rhodopirellula baltica Phyre2 PDB 2vbu chain A domain 1 Region: 41 - 53 Aligned: 13 Modelled: 13 Confidence: 10.5% Identity: 31% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Riboflavin kinase-like Family: CTP-dependent riboflavin kinase-like Phyre2 PDB 3gku chain B Region: 50 - 61 Aligned: 12 Modelled: 11 Confidence: 8.8% Identity: 50% PDB header:rna binding protein Chain: B: PDB Molecule:probable rna-binding protein; PDBTitle: crystal structure of a probable rna-binding protein from clostridium2 symbiosum atcc 14940 Phyre2 PDB 2yy0 chain D Region: 69 - 98 Aligned: 30 Modelled: 30 Confidence: 7.9% Identity: 23% PDB header:transcription Chain: D: PDB Molecule:c-myc-binding protein; PDBTitle: crystal structure of ms0802, c-myc-1 binding protein domain2 from homo sapiens Phyre2 PDB 1hyv chain A Region: 49 - 55 Aligned: 7 Modelled: 7 Confidence: 7.4% Identity: 57% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1in0 chain A domain 2 Region: 85 - 100 Aligned: 16 Modelled: 16 Confidence: 7.2% Identity: 6% Fold: Ferredoxin-like Superfamily: YajQ-like Family: YajQ-like Phyre2 PDB 3cta chain A domain 2 Region: 44 - 53 Aligned: 10 Modelled: 10 Confidence: 7.1% Identity: 40% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Riboflavin kinase-like Family: CTP-dependent riboflavin kinase-like Phyre2 PDB 2kxw chain B Region: 84 - 100 Aligned: 17 Modelled: 17 Confidence: 6.0% Identity: 53% PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2 Phyre2 PDB 1w7p chain D domain 1 Region: 39 - 54 Aligned: 16 Modelled: 16 Confidence: 5.4% Identity: 31% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Vacuolar sorting protein domain Phyre2 1 c4a19Q_ 2 c3izck_ 3 c3iz5k_ 4 c3b5mD_ 5 d2vbua1 6 c3gkuB_ 7 c2yy0D_ 8 d1hyva_ 9 d1in0a2 10 d3ctaa2 11 c2kxwB_ 12 d1w7pd1

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