Table 3. Predicted regulatory RNAs that have supporting literature evidence.

Ranka	GI	RSSVMb	RNAzb	QRNA (Q) Terminator (T) Attenuator (A)	Gene Name	Gene Product	Knowledge of Regulation	Reference
5	24350784	1.000	0.998	Q T -	ilvG	acetolactate synthase II, large subunit	Leader peptide, and transcription attenuator	[48]
17	24346570	1.000	0.507	- T A	ldhA	D-lactate dehydrogenase	Possible post-transcriptional effect	[56]
23	24348431	1.000	0.105	- T -	aspS	aspartyl-tRNA synthetase	tRNA synthetase leader
25	24348233	1.000	0.904	- - -	ilvI	acetolactate synthase III, large subunit	Leader peptide, and transcription attenuator	[48]
26	24349427	1.000	0.862	- - -	flgB	flagellar basal-body rod protein FlgB	Putative GEMM element	[20]
27	24348700	1.000	0.241	- - -	aroH	phospho-2-dehydro-3-deoxyheptonate aldolase, trp-sensitive	Possible transcription termination	[57]
35	24350656	1.000	0.998	Q T A	leuA	2-isopropylmalate synthase	Leader peptide, and transcription attenuator	[48]
41	24345882	1.000	0.094	- - -	pdhR	pyruvate dehydrogenase complex repressor	PdhR-box in E. coli	[58]
52	24348056	1.000	0.893	- T -	adhE	aldehyde-alcohol dehydrogenase	Stem-loop for occupying RBS in E. coli	[59]
55	24346560	1.000	0.196	- - -	ahpC	Alkyl hydroperoxide reductase, C subunit	Post-transcriptionally regulated by CsrA in Helicobacter pylori	[60]
63	24347612	1.000	0.012	Q T A	glnS	glutaminyl-tRNA synthetase	tRNA synthetase leader	[61]
83	24347590	0.998	0.451	- T A	SO1769	glutamate decarboxylase, putative	Possible post-transcriptional regulation in S. oneidensis	[47]
88	24345631	0.998	0.999	Q T -	rpoB	DNA-directed RNA polymerase, beta subunit	Transcriptional attenuation	[62],[63]
91	24345625	0.998	1.000	- - -	rplJ	ribosomal protein L10	Ribosomal protein leader	Rfam
105	24349015	0.994	0.274	Q T -	pflB	formate acetyltransferase	Possible post-transcriptional regulation	[64]
106	24350214	0.994	0.688	- - -	SO3896	Outer membrane porin, putative	Post-transcriptional regulation in S. oneidensis	[65]
109	24345633	0.992	0.988	Q T A	rpsL	ribosomal protein S12	Ribosomal protein leader	[32]
112	24349403	0.990	0.179	- T -	fliE	flagellar hook-basal body complex protein FliE	Putative GEMM element	[20]
124	24345621	0.987	0.108	- T -	secE	preprotein translocase, SecE subunit	RNaseIII sites in the leader sequence of SecE in E. coli	[66]
147	24347716	0.972	0.456	- T -	speA	biosynthetic arginine decarboxylase	Possible post-transcriptional regulation in S. oneidensis	[47]
161	24347079	0.958	0.524	Q - -	aroF	phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive	Attenuator sensing tyr-tRNA	[67]
163	24349925	0.956	0.102	- - -	rplU	ribosomal protein L21	Ribosomal protein leader	[32]

^{a, b}same as those in Table 2.