**Supplementary Information**

**Full results of functional analysis of disordered regions in *** Saccharomyces cerevisiae* can be found here.

The columns show the Gene Ontology (GO) number, the number of times the GO term is used to describe a yeast protein in the set of translated open reading frames, the number of times the GO term is found associated with a disordered region and the mean and standard deviation for the occurrence of the GO term in random simulations. This is followed by the number of simulations where Z-scores greater and lesser than the disorder score are obtained, and finally the p-value of the disorder predictions under the null model.

The terms that describe fewer than 25 proteins are not given a p-value, since the score distribution cannot be approximated as continuous below this threshold. The terms that are marked with an asterisk annotate more than 50 yeast proteins and are statistically significant (P less than 0.05) after a Bonferroni adjustment for multiple hypothesis tests. The Bonferroni corrections were carried out for each ontology separately, with estimates of the number of independent hypotheses k, obtained by counting the number of terminal nodes that annotate more than 50 proteins. These terminal nodes do not have any descendents in the directed acyclic graph that also annotate more than 50 proteins. This gave estimates for k of 27, 48 and 25 for the molecular function, biological process and cellular component ontologies, respectively.

### Figure 1

Fraction of proteins in the Archaea, Eubacteria and Eukaryota that contain predicted disordered segments of length greater or equal to thresholds which vary from 0 to 100 residues. For example, around 0.1 (10%) of eukaryote proteins are predicted to have a disordered segment of length greater than or equal to 90 residues.

### Figure 2

Cumulative distribution of disorder composition for the three kingdoms of life. A factor of around 0.2 of eukaryote proteins, for example, are more than 30% disordered.

**Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF and Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life Journal of Molecular Biology, 337, 635-645.**