Table 2. Predicted regulatory RNAs that match the known cis-regulatory RNA elements or genes in the Rfam database.
| Ranka | GI | RSSVMb | RNAzb | QRNAc | Gene Name | Gene Product | Matching RNA Family in Rfam | ||
| 1 | 24349136 | 1.000 | 1.000 | +d | trpE | anthranilate synthase component I | RF00513 | Trp_leader | RNA element |
| 3 | 24346870 | 1.000 | 1.000 | +d | SO1202 | conserved hypothetical protein | RF00005 | tRNA | tRNA |
| 4 | 24351250 | 1.000 | 0.998 | +d | SO4727 | conserved hypothetical protein | RF00558 | L20_leader | RNA element |
| 6 | 24347627 | 1.000 | 0.998 | ppiD | peptidyl-prolyl cis-trans isomerase D | RF00506 | Thr_leader | RNA element | |
| 7 | 24349634 | 1.000 | 0.997 | +d | thrA | aspartokinase I/homoserine dehydrogenase, threonine-sensitive | RF00506 | Thr_leader | RNA element |
| 8 | 24347975 | 1.000 | 0.997 | + | hisG | ATP phosphoribosyltransferase | RF00514 | His_leader | RNA element |
| 16 | 24347418 | 1.000 | 0.523 | rpsB | ribosomal protein S2 | RF00127 | t44 RNA | RNA gene | |
| 34 | 24346699 | 1.000 | 1.000 | + | SO1071 | conserved hypothetical protein | RF00080 | yybP-ykoY | Riboswitch |
| 39 | 24347085 | 1.000 | 0.997 | + | pheA | chorismate mutase/prephenate dehydratase | RF00513 | Trp_leader | RNA element |
| 64 | 24346616 | 1.000 | 1.000 | + | SO1007 | conserved hypothetical protein | RF00168 | Lysine | Riboswitch |
| 73 | 24348868 | 0.999 | 0.240 | + | Rne | ribonuclease E | RF00370 | sroD RNA | RNA gene |
| 93 | 24346037 | 0.997 | 0.678 | SO0547 | conserved hypothetical protein | RF00522 | PreQ1 | Riboswitch | |
| 100 | 24348781 | 0.995 | 0.986 | SO2715 | TonB-dependent receptor | RF00059 | TPP | Riboswitch | |
| 117 | 24350326 | 0.989 | 0.765 | +d | lysC | aspartokinase III, lysine-sensitive | RF00168 | Lysine | Riboswitch |
| 120 | 24348446 | 0.989 | 0.420 | thiC | thiamin biosynthesis protein ThiC | RF00059 | TPP | Riboswitch | |
| 125 | 24347051 | 0.987 | 0.969 | nadB | L-aspartate oxidase | RF00522 | PreQ1 | Riboswitch | |
| 133 | 24346318 | 0.982 | 0.690 | SO0774 | 5-formyltetrahydrofolate cyclo-ligase family protein | RF00013 | 6S RNA | RNA gene | |
| 195 | 24346874 | 0.903 | 0.014 | rpsO | ribosomal protein S15 | RF00114 | S15 leader | RNA element | |
| 302 | 24346370 | 0.661 | 0.820 | + | SO0815 | TonB-dependent receptor C-terminal domain protein | RF00174 | Cobalamin | Riboswitch |
| Total counts | 17 | 16 | 11 | ||||||
a
The rank is based on the P-value of RSSVM.
b
Bold fonts represent predictions above the P-value cutoff for RSSVM (0.95) or RNAz (0.50).
c
“+” represent QRNA predictions that fit the “RNA” model in at least two pairwise alignments.
d
The shuffled sequences were identified as “RNA” by QRNA.