Table 3.

Dipeptide similarity matrix for a representative sampling of taxa from the PheRS sequence alignmenta

OrganismSimilarity to:
123456789101112131415
 1. E. coli
 2. R. prowazeckii 15.3
 3. B. subtilis 18.811.7
 4. C. tepidum 13.510.415.8
 5. D. radiodurans 13.98.010.611.4
 6. T. maritima 15.611.413.014.412.4
 7. A. aeolicus 15.010.315.813.511.317.6
 8. B. burgdorferi 3.33.54.33.94.75.83.1
 9. P. horikoshii 5.45.44.55.72.85.14.514.3
10. M. jannaschii 5.27.14.07.26.06.74.412.425.0
11. M. thermoautotrophicum 6.04.04.25.54.73.75.611.620.426.3
12. A. fulgidus 5.14.35.56.05.26.26.712.319.620.424.7
13. S. solfataricus 4.75.25.17.73.56.74.412.714.216.717.112.6
14. A. pernix 4.52.73.36.75.04.65.18.812.916.215.114.321.0
15. S. cerevisiae 2.32.92.02.32.82.52.67.16.59.58.98.79.17.7
16. C. elegans 2.33.32.53.93.74.14.17.09.911.211.512.312.110.227.0
  • a A dipeptide similarity matrix resembles a normal amino acid similarity matrix except that adjacent columns in the alignment are considered in pairs (dipeptides), not singly. Only dipeptide identities between sequences are scored. The rationale for using two adjacent columns as the unit measured is that doing so takes the actual sequence of the molecule into account whereas treating the columns singly does not (i.e., shuffling columns does not change the results of the analysis in the latter case but does so in the former).