A. Organization of genes encoding the putative thermophyle-specific DNA repair system in two Thermus strains and the draft genome of D. geothermalis. The boxes on top of the figure show COG numbers. Genes are shown by block arrows indicating the direction of transcription and identified by their systematic names. For each column of the alignment, the corresponding COG number and predicted function is indicated. D. geothermalis' genes are connected with respective orthologs in both TT strains by a straight line. Generally, orthologous genes are shown by the same color and pattern. The exceptions are the RAMP proteins of COGs 1336, 1367, 1604, 1337 and 1332, which are all shown in pink. Other, more distant RAMPs are also shown in pink, with different patterns . Proteins that do not belong to COGs but have homologs in other species are marked by diamonds. Abbreviations: HEL, predicted helicase, HD nuclease – HD conserved motif containing predicted nuclease conserved region; POL – novel predicted polymerase, RECB – predicted nuclease of RecB family; B. Comparison of gene organization in the region of the megaplasmid coding for reverse gyrase in two TT strains. The shorter gyrase gene in HB27 indicates truncation. Abbreviations: REVGYR, reverse gyrase, MET_PR – predicted metal-dependent protease; REC_DNA – three-domain fusion protein (DnaQ endonuclease, DinG helicase, and RecQ helicase).
Omelchenko et al. BMC Evolutionary Biology 2005 5:57 doi:10.1186/1471-2148-5-57