Table 1. Transcriptional start sites for analyzed genes and their possible −10 elements.

name	promoter	references	involved TFs	data mapping (TSS and −10 element)	ATG dist.	sigma scores1	inferred boxes	Additional evidence
glk	glkP1k-P2n	[36], in this work	FruR	GCGTTGTTGTTATGCCCCCAGGTATTTACAGTGTGAGAA	−36	s70: 3.92	s382	C
	glkP3n-P4n	in this work		CCCCCAGGTATTTACAGTGTGAGAAAGAATT ATTTTGAC	−21	s38: 2.95	s703	A,C
pgi	pgiP1k-P2n	[37], in this work		ACCATCACATTTTTCTGTGACTGGCGCTACAATCTTCCA	−36	s70: 6.9; σ38: 7.44	-	A,B,E
pfkA	pfkAP1k-P2n	[39], in this work	FruR	ATCAATTCAGCAGGAAGTGATTGTTATACTATTTGCACA	−78	s70: 8.61; σ38: 5.7	-	A,B
	pfkAP3n-P4n	in this work		TCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTC	−29	s70: 1.12	s382	A,E
tpiA	tpiAPki	[40]		CTGCCCTGCGGGGCGGCCATCTTCCTTTATTCGCTTATA	−19	-	-	-
	tpiAP1n-P2n	in this work		CAAAGCCTTTGTGCCGATGAATCTCTATACTGTTTCACA	−62	s70: 8.07; σ38: 7.4	-	A,E
gapA	gapAP1k-P1an	[41], [43], in this work		CGCTTGACGCTGCGTAAGGTTTTTGTAATTTTACAGGCA	−36	s70: 3.76; σ38: 0.82	-	A,B,D
	gapAP2k	[41], [43]		CCTTTAAAATTCGGGGCGCCGACCCCATGTGGTCTCAAG	−153	-	-	A
	gapAP3k	[41], [43]	Crp	TCACATTTTTATCGTAATTGCCCTTTAAAATTCGGGGCG	−174	-	-	-
	gapAP4k	[41], [43]		AACACCAACTGGCAAAATTTTGTCCTAAACTTGATCTCG	−245	-	-	-
epd	epdP1k-P2	[45], in this work	FruR, Crp	ACATTCCTTTTATTCCACGTTTCGCTTATCCTAGCTGAA	−132	no predictions	s703,σ382	A,D
pgk	pgkP1k	[45]		AAGCAGCACAAGGTGCATTTCATGGTATAGTTGACTATA	−235	-	-	A
	pgkP2n	in this work		TGTTGCTTTCAGGTAAGACGCAAGCAGCGTCTGCAAAAC	−26	no predictions	-	D,E
	pgkP3n	in this work		GCACACCTGATCAAAACGTTGGTCTGGTGCGATAACGAA	−113	no predictions	s703	A,D
gpmA	gpmAP1ki-P2n	[46], in this work	Fur	AAGCATTGCTGTTGCTTCGTCGCGGCAATATAATGAGAA	−37	s70:7.56; σ38: 3.66	-	A
	gpmAP3n-P4n	in this work		CCTTACACTGCGCCACTATTTTCGCTATGGTTATGCGTA	−75	s70:5.80; σ38: 7.48	-	-
eno	enoP1k	[47]		AATCGTGTCAGCGTCAACATCAAACTGATCGATTCACAA	−731	-	-	-
	enoP2k	[47]		CGAAGCACTGAAACACGGTGGGCTGAAGAATCGTGTCAG	−760	-	-	-
	enoP3k	[47]		TAAACGATTCAGCTTAAACTGCCCGGAAGCGAATCTGTC	−903	-	-	-
	enoP4n-P5	in this work		GCGTACCCTGGGTACGCGTTGTTTGTCTGGAGTTTCAGT	−27	no predictions	s703,σ382	A,D,E
	enoP6n	in this work		GAGTTCCAGAAACGTCAGGCGAAGTAAGTAAAAAAGTTA	−77	no predictions	-	D
	enoP7n-P8n	in this work		GGGGATGATCAGTTGGTCGAGATCATCGAAGTTCCGAAT	−212	no predictions	s703,σ382	D
pykF	pykFPΠκι	[49]	FruR	TGTTTTCCTTTTGGATTAATTTCAGCGTATAATGCGCGC	−231	-	-	-
	pykFP1n-P2n	in this work		GGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTC	−34	no predictions	s703,σ382	A,B,D
	pykFP3n	in this work		GATGTCACCTATCCTTAGAGCGAGGCACCACCACTTTCG	−80	no predictions	-	D
	pykFP4n-P5n	in this work		CCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCG	−97	s70: 4.79; σ38: 9.95	-	B,D
pykA	pykAP1n-P2n	in this work		AAGTGACGATCGCTAAAAACGACTGTCACTGTCCTAATC	−105	s70: 0.90	s382	B,D
	pykAP3n-P4n	in this work		GTCAAAGAAGCGCTGAAGGAATCGCGTTTTGATAAGCAG	−153	s70: 1.76	s382	A,B,D
pdhR	pdhRP1k-P2n	[51]–[52], in this work	Crp, Fnr, PdhR	GTATGGACATAAGGTGAATACTTTGTTACTTTAGCGTCA	−58	no predictions	s703,σ382	B,D
aceE	aceEP1k-P2n	[50], in this work		AACCTGTCTTATTGAGCTTTCCGGCGAGAGTTCAATGGG	−48	s70: 1.90	s382	-
poxB	poxBP1k-P2n	[57], [58], in his work	MarA, SoxS	TCCCTTCCCCCTCCGTCAGATGAACTAAACTTGTTACCG	−27	s70: 5.31; σ38: 9.5	-	B,C
acs	acsP1k	[60]–[61]	Fis, Crp, Ihf	TCTTTAATCAATTGTAAGTGCATGTAAAATACCACTTTA	−224	-	-
	acsP2k-P3n	[60]–[61], in this work	Fis, Crp, Ihf	CCCCTACATTTAACGCTTATGCCACATATTATTAACATC	−20	s70: 4.03; σ38: 4.97	-	B,C
			consensus sequences	sigma 70:TGGTATAATG sigma 38:CTACACTT

Proposed promoters in which putative σ⁷⁰ and σ³⁸ overlapping recognition sequences have been determined, are presented as bold sequences.

The transcription start site (TSS) for each gene is underlined at the end of each nucleotide sequence. (1) predictions were obtain with PWMs (σ⁷⁰ and σ³⁸) analyzed in meta-MEME software and inferred (2) by visual comparison using the −10 sigma 38 consensus sequence by Weber, H. et al. [5]. (3) in these cases, σ⁷⁰ promoter sequences were inferred using the −10 sigma 70 consensus sequence. (n) new data obtained in this work; (k)known data; (ki) previously inferred promoters not detected in this work. Additional evidence that supports the functionality of the proposed promoters detected by 5′RACE: (A) global mapping of TSS; (B) in vitro transcription; (C) obtained with two tags; (D) repeated experiments and (E) promoter fusions to a reporter gene. TFs, transcriptional factors.