TABLE 2.
Top 10-ranked putative target genes for csRNA1-1 and csRNA1-2
| Ranka | Energy | Locus tag | Gene description (gene) | Putative interaction between targets and csRNA1-1 or csRNA1-2b |
|---|---|---|---|---|
| 1 (1) | −15.87 | SSA_2317 | Tfp pilus assembly protein, pilus retraction ATPase PilT | csRNA1-1 47 ACUUUUUCAAAUCCUAA 31 |
| |:::||||||||||| | ||||
| SSA_2317 −14 AGGGGAAGUUUAGGAUG 3 | ||||
| 2 (2) | −14.36 | SSA_2345 | Hypothetical protein | csRNA1-1 60 ACCCUCUAAUAAUACU 45 |
| |||||||| ||||| | ||||
| SSA_2345 −11 AGGGAGAUU-UUAUGU 4 | ||||
| 3 (3) | −14.01 | SSA_2216 | Lipopolysaccharide biosynthesis protein (licD1) | csRNA1-1 52 UAAU-ACUUUUUCAAAUCCUA 32 |
| |||| |||||||||||:||| | ||||
| SSA_2216 −30 AUUAUUGAAAAAGUUUGGGAG −10 | ||||
| 4 | −13.14 | SSA_1763 | Molybdenum ABC transporter ATPase | csRNA1-1 35 CCUAAUAGUUUGU 23 |
| ||||||||||| | ||||
| SSA_1763 8 AGAUUAUCAAACU 20 | ||||
| (4) | −13.19 | SSA_1655 | Hypothetical protein | csRNA1-2 23 UUCAAUCCUCC 13 |
| ||||||||| | ||||
| SSA_1655 −78 CAGUUAGGAGA −68 | ||||
| 5 (5) | −12.43 | SSA_2217 | Cps9H | csRNA1-1 48 UACUUUUUCAAAUCCUA 32 |
| ||| |||||||||||| | ||||
| SSA_2217 −27 AUG-AAAAGUUUAGGAA −11 | ||||
| 6 (6) | −11.89 | SSA_1635 | Hypothetical protein | csRNA1-1 62 CCUCUAAUAAUACUUUU 46 |
| ||| |||||||||||| | ||||
| SSA_1635 2 GGAAAUUAUUAUGAAAU 19 | ||||
| 7 (7) | −11.64 | SSA_0227 | Collagen-binding surface protein | csRNA1-1 60 ACC-CUCUAAU-AAUACUUUU 42 |
| || |:||||| ||||| ||| | ||||
| SSA_0227 −14 CGGAGGGAUUAUUUAUG-AAA 6 | ||||
| 8 | −11.39 | SSA_1820 | Hypothetical protein | csRNA1-1 19 AAUCCCCCG 11 |
| ||||||| | ||||
| SSA_1820 4 AUAGGGGGA 12 | ||||
| 37 (8) | −11.59 | SSA_0718 | Hypothetical protein | csRNA1-2 23 UUCAAUCCUCCAGA 10 |
| |||||||| ||: | ||||
| SSA_0718 −78 CAGUUAGGAAGUUA −65 | ||||
| 9 (9) | −11.36 | SSA_1632 | Surface protein | csRNA1-1 59 CCCUCUAAUAAUACUU 44 |
| |||||||| |||| | ||||
| SSA_1632 −11 AGGAGAUUAAAAUG-A 4 | ||||
| 10 | −11.16 | SSA_0991 | DNase | csRNA1-1 51 UAAUACUUUUUCAAAUCCU 33 |
| ||||||||||||||||| | ||||
| SSA_0991 −3 UUUAUGAAAAAGUUUAGGU 16 | ||||
| (10) | −11.35 | SSA_2177 | Hypothetical protein | csRNA1-2 51 ACUUUUUCAA-AUCCU 37 |
| ||||||||| |||: | ||||
| SSA_1702 4 AGAAAAAGUUACAGGG 19 |
a
Rank for csRNA1-2 is indicated in parentheses.
b
Vertical lines and dots between nucleotides of mRNA and csRNA indicate standard (Watson-Crick) and nonstandard (G-U wobble) base-pairing interactions, respectively.