TABLE 4.

Operons containing genes with putative σ⁵⁴ promoters

Gene type	First gene in operon	Relevant gene	No. of genes in operon	σ54 promoter sequencea	Reference
Genes known to be required for A motility	MXAN2991	aglZ	1	TGGCAAC-N4-CTGCT	34
	MXAN3502	agmI	2	TGGGGCG-N4-TTGCC	35
	MXAN4799	agmC	2	TGACAGA-N4-TTTCA	35
	MXAN5818	agmR	2	TGGCACA-N4-GTGCT	35
	MXAN5820	agmM	1	TGGCCCT-N4-CTGCT	35
Genes known to be required for sporulation	MXAN2269	mspA	1	TGGCCTA-N4-GTGCT	3
	MXAN3225	exo	5	TGGCACA-N4-CTGCT	21
	MXAN5432	tps	2	TGGGGCA-N4-TTGCT	18

^aThe putative promoter regions of operons containing A-motility and sporulation genes were analyzed using the M. xanthus genome sequence (5) and PromScan (http://molbiol-tools.ca/promscan/), a bioinformatics tool that was specifically developed to identify σ⁵⁴-RNA polymerase binding sites in the sequences of bacterial DNA. To be designated a σ⁵⁴ promoter, there had to be a potential binding site for σ⁵⁴-RNA polymerase and a potential EBP binding site, which is a tandem repeat of at least 7 bp (27). On the basis of tests done with known promoter sequences and intragenic sequences, we estimated that our analysis had a false-positive rate of about 4% and a false-negative rate of about 23%. The −12 and −24 regions of the putative σ⁵⁴ promoters are shown. Bold, underlined nucleotides are those that match nucleotides in the σ⁵⁴ consensus sequence, which is TGGCACG-N4-TTGC(T/A) (1).