The comparison of T. velox with T. acidaminovorans reached the highest scores using the GGDC, 44% of the average of genome length are covered with HSPs (Table 5). The identity within the HSPs was 78%, whereas the identity over the whole genome was 35%. Lower similarity scores were observed in the comparison of T. velox with A. http://www.selleckchem.com/products/MLN8237.html paucivorans, only 17% of the average of both genome lengths are covered with HSPs. The identity within these HSPs was 77%, whereas the identity over the whole genome was only 13%. With regard to T. velox and T. acidaminovorans the corresponding DDH estimates were below the 70% threshold under formulas 1-3 throughout: 27.2% (��3.5), 20.4% (��2.3) and 24.6% (��3.0). The DDH estimated confidence intervals are given in parentheses as provided by [41].
These results are in line with a previously reported wet-lab DDH value of 15% (��1) [1] As expected, those distances relating HSP coverage (formula 1) and number of identical base pairs within HSPs to total genome length (formula 3) are higher between the T. velox and T. acidaminovorans than between T. velox and A. paucivorans. That the distances relating the number of identical base pairs to total HSP length (formula 2) behave differently indicates that the genomic similarities between T. velox, T. acidaminovorans and A. paucivorans are strongly restricted to more conserved sequences, a kind of saturation phenomenon [42]. In order to compare the T. velox and T. acidaminovorans genomes, correlation values (Pearson coefficient) according to the similarity on the level of COG category, pfam and TIGRfam were calculated.
A very high correlation value (0.98) was reached on the level of pfam data; the correlation values on the basis of COG and TIGRfam data were only slightly smaller; 0.95 and 0.97, respectively. As a correlation value of 1 indicates the highest correlation, we can find a near perfect correlation between the genomes of T. velox and T. acidaminovorans considering the above data [40]. The comparison of the number of genes belonging to different COG categories revealed no large differences in the genomes of T. velox and T. acidaminovorans, with only 0.2% deviation between the same COG categories on average. A slightly higher fraction of genes belonging to the categories amino acid metabolism (T. velox 11.8%, T. acidaminovorans 11.4%), carbohydrate metabolism (T. velox 5.
7%, T. acidaminovorans 5.3%) and defense mechanisms (T. velox 1.0%, T. acidaminovorans 0.7%) were identified in T. velox. The gene count in further COG categories such as cell cycle control, cell motility, cell biogenesis, lipid metabolism, secondary catabolism, posttranslational modification and signal transduction was also slightly increased in T. velox, but differed at most by 5 genes. In contrast, Dacomitinib a slightly smaller fraction of genes belonging to the categories translation (T. velox 8.8%, T. acidaminovorans 9.2%), nucleotide metabolism (T. velox 3.7%, T. acidaminovorans 4.