Table 4.
The %G in mmt alignments is predicted by the presence of G-specific (first two rows) and G-favored (last two rows) interactions, some of which are in bacterial and mmt 3D structures
| Interactions present in E. coli and S. scrofa 3D structures | Interactions only present in in E. coli 3D structure | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Number of positions forming the interaction | Number of nucleotides by color | Average %G | Number of positions forming the interaction | Number of nucleotides by color | Average %G | |||||||
| Type of interaction | (Number of positions forming additional interactions in E.c./S.sc.) | Blue (High/ High) | Cyan (High/ Interm) | Yellow (High/ low) | Bact | mmt | (Number of positions forming additional interactions in E.c./S.sc.) | Blue (High/ High) | Cyan (High/ Interm) | Yellow (High/ low) | Bact | mmt |
| Base-phosphate | 21 (16/16) | 15 | 6 | 0 | 99.6 | 89.0 | 18 (12/13) | 0 | 3 | 15 | 99.2 | 6.2 |
| G-Ribose or GU Packing Interactions | 17 (6/5) | 10 | 5 | 2 | 99.5 | 80.0 | 8 (2/1) | 0 | 1 | 7 | 98.2 | 6.1 |
| 3° and Multi-Helix Junction Stacking and Intercalation | 38 (25/23) | 22 | 9 | 7 | 99.0 | 69.0 | 1 (0/0) | 0 | 0 | 1 | 99.1 | 5.1 |
| Non-WC Pair or 3°WC pair | 71 (36/30) | 40 | 14 | 17 | 99.3 | 66.4% | 19 (9/10) | 2 | 4 | 13 | 99.3 | 20.3 |
| RNA–protein interaction | 22 (16/14) | 14 | 0 | 8 | 99.2 | 63.8 | 14 (9/9) | 2 | 4 | 8 | 99.5 | 32.5 |
| Total number of interactions | 169 | 101 | 34 | 34 | 0 | 4 | 12 | 44 | ||||
| Total number of nucleotides | 126 | 68 | 27 | 31 | 50 | 4 | 11 | 35 | ||||
All selected positions have high G composition in bacteria. Rows correspond to different types of G-stabilized interactions; the first two rows are G-specific, and the rest are G-favored interactions. The first set of columns cover cases where the interaction is present in both bacteria and mmt; the second set of columns covers cases where the interaction is lost in mmt. The first set of columns includes all positions for which the corresponding bases in the E. coli and S. scrofa 3D structures form the same G-stabilized interaction and the second set of columns, those for which only the E. coli base does so. The number of nt positions is reported along with the average %G of the respective columns from the two alignments. We note that many nts with high-G make more than one G-stabilized interaction and are included in more than one row. The number of positions that form additional interactions in each structure is shown in parentheses after the nt count. There are also positions where the S. scrofa structure lacks G that may be found in other mmt sequences. If the interaction is nonetheless observed in S. scrofa, it is included in the first set of columns; if not, it goes to the second set of columns.