Table 1.

Top 10 predicted targets of Ec-rnTrpL, based on the CopraRNA p-value. For each gene, 200 nt upstream and 100 nt downstream of the first nucleotide of the coding region are extracted as 5ʹUTR for target prediction. The interaction site coordinates are given relative to the first nucleotide of the coding region. Positive coordinates indicate interaction in the coding regions. In case of operons, negative numbers might indicate an interaction within the predecessor gene in the operon. ¹The upstream gene sanA was tested, in which the interaction site is located; ²mhpC was tested, although the interaction site is located in the upstream gene mhpB (see Fig. 4); NA, not applicable

p-value	Locustag	Gene	Interaction site borders in mRNA	Experimentally tested	Regulation	Annotation
6,55E-09	b3702	dnaA	+12 to + 87	yes	negative	chromosomal replication initiator protein DnaA
2,58E-05	b0905	ycaO	+70 to +89	yes	no effect	ribosomal protein S12 methylthiotransferase accessory factor YcaO
5,32E-05	b2145	sanA/yeiS	−180 to −142	yes	negative1	DUF2542 domain-containing protein YeiS
7,95E-05	b0349	mhpB/mhpC	−200 to −177	yes	positive2	2-hydroxy-6-ketonona-2 4-dienedioate hydrolase
0,000186	b2182	bcr	−74 to −20	no	NA	multidrug efflux pump Bcr
0,000189	b0661	miaB	−200 to −185	no	NA	isopentenyl-adenosine A37 tRNA methylthiolase
0,000368	b3052	rfaE	−95 to −87	no	NA	fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase
0,000433	b2465	tktB	−178 to −169	no	NA	transketolase 2
0,000488	b1888	cheA	−1 to +6	no	NA	chemotaxis protein CheA
0,000766	b2808	gcvA	−142 to −118	no	NA	DNA-binding transcriptional dual regulator GcvA