The selection and plot below are almost the same as the single sequence predictions, refer to the single sequence tutorial for the main functionality. Hovering over the plot, however, will display the Gaussian Mixture Model (GMM) score for that residue. This score is based on an analysis of the 7-dimensional 'biophysical space' for that residue, in relation to the column it occupies in the MSA. High scores indicate very normal scores, low (negative) scores indicate unusual scores, meaning this residue is unlike other ones in the alignment. Below the plot, you will also find a breakdown of the residues that are indicated by the GMM as unusual, using 5%, 1% and 0.1% cutoffs over the full MSA..
Select protein ( available):
Click on the above prediction names to toggle them on/off
The above plot shows the following predictions for :
|DynaMine backbone dynamics||Values above 0.8 indicate rigid conformations, values above 1.0 membrane spanning regions, values below 0.69 flexible regions. Values between 0.69-0.80 are 'context' dependent and capable of being either rigid or flexible.|
|DynaMine sidechain dynamics||Higher values mean more likely rigid. These values are highly dependent on the amino acid type (i.e. a Trp will be rigid, an Asp flexible).|
|DynaMine conformational propensities (sheet, helix, coil, ppII (polyproline II))||Higher values indicate higher propensities.|
|EFoldMine earlyFolding propensity||Values above 0.169 indicate residues that are likely to start the protein folding process, based on only local interactions with other amino acids.|
|Disomine disorder||Values above 0.5 indicate that this is likely a disordered residue.|
The plot below shows, for the protein you selected above, the variation in predicted biophysical parameters within the multiple sequence alignment (MSA) that you uploaded. This variation is displayed according to simple box plot statistics, with median, first/third quartile, and outlier range of the distributions shown. Columns in the MSA that are 'gapped' for the selected protein are not shown here. In other words, what is displayed is how the biophysical prediction for each aligned position varies for all the proteins that are in the MSA. You can select the type of prediction that you want to display in the selection box below the plot, and turn each distribution statistic on and off by clicking on its name. The 'prediction' field corresponds to the same type of prediction shown in the top plot.
The above plot shows multiple sequence alignment (MSA) derived distributions of the prediction type you selected, organised by the protein you selected for the top graph. The distributions are based on an analysis of the uploaded MSA, and shows the 'evolutionary allowed' range for this prediction. The red line corresponds to the single protein prediction in the top graph, the other lines show simple statistical parameters calculated from the values per MSA column. Values of the red line outside of the quartile range therefore indicate rather unusual behavior for this particular protein compared to its homologues in the MSA.
If you now select the following characteristics in the dropdown box above, and compare the values for the natural TIM barrel proteins to the de novo designed sTIM-11 protein, and for the misfolding OctaV1 protein (select these at the top of the page):