Table 1. Open in new tab Significant...

Gene	Product	−24 Motifs	−12 Motifs	References
	Flagellar assembly
flgA	Flagellar basal body P-ring formation chaperone FlgA	TCGGCA	TTGCTT	[33, 40]
flgB	Flagellar basal body rod protein FlgB	TTGGCA	TTGCTA	[33, 40]
flgF	Flagellar basal-body rod protein FlgF	TTGGTT	TTGCTT	[33, 40]
flgG	Flagellar basal-body rod protein FlgG	ATGGCT	TTGCAA	[40]
fliE	Flagellar hook-basal body complex protein FliE	CTGGCA	TTGCTT	[33]
motA	Flagellar motor stator protein MotA	TTGGTT	TGGCAT	[34]
	Metabolism
PP_2783	3-oxoacyl-ACP reductase family protein	TGGGCT	TGGCAT	[41]
eutC	Ethanolamine ammonia-lyase subunit EutC	TTGGCA	TTGCAT	[39]
PP_1786	Glycosyltransferase	ATGGCA	TTGCAT	[38]
PP_0859	Amidohydrolase	CTGGTA	GTGCTT	[36]
edd	Phosphogluconate dehydratase	GTGGCA	TTGTTT	[40]
PP_2836	Fumarylacetoacetate hydrolase family protein	GTGGCT	TTGCAA	[33]
PP_1946	Glucose 1-dehydrogenase	TTGGCA	TTGCAA	[33]
PP_3486	Cytochrome c	ATGGCT	GTGCTT	[40]
PP_1141	ABC transporter substrate-binding protein	TGGGCT	TGGCAT	[40]
ppx	Exopolyphosphatase	ATGGCA	TTGCAT	[42]
PP_3778	Pyrroline-5-carboxylate reductase	TTGACA	TTGCTA	[35]
xdhA	Xanthine dehydrogenase small subunit	TGGGCA	GTGCAT	[37]
	Transport
PP_4970	Cytochrome c	GTGGCT	GTGTTT	[40]
ntrB	Nitrogen regulation protein NR(II)	GTGGTT	TTGCAT	[40]
	Response to stress
PP_3248	Dyp-type peroxidase	TTGATA	TTGCAA	[38]
PP_3539	MerR family DNA-binding transcriptional regulator	GTGGTT	TTGAGT	[40]
	Transcription regulation
PP_2952	LysR family transcriptional regulator	GTGGTT	TGGCAT	[40]
PP_0952	RNAP σ⁵⁴	AAGGCA	TTGCTT	[40]
	Uncharacterized
PP_1450	HlpA activation/secretion protein HlpB	GTGGCT	TAGCAT	[40]

Gene

Product

−24 Motifs

−12 Motifs

References

Flagellar assembly

flgA

Flagellar basal body P-ring formation chaperone FlgA

TCGGCA

TTGCTT

[33, 40]

flgB

Flagellar basal body rod protein FlgB

TTGGCA

TTGCTA

[33, 40]

flgF

Flagellar basal-body rod protein FlgF

TTGGTT

TTGCTT

[33, 40]

flgG

Flagellar basal-body rod protein FlgG

ATGGCT

TTGCAA

[40]

fliE

Flagellar hook-basal body complex protein FliE

CTGGCA

TTGCTT

[33]

motA

Flagellar motor stator protein MotA

TTGGTT

TGGCAT

[34]

Metabolism

PP_2783

3-oxoacyl-ACP reductase family protein

TGGGCT

TGGCAT

[41]

eutC

Ethanolamine ammonia-lyase subunit EutC

TTGGCA

TTGCAT

[39]

PP_1786

Glycosyltransferase

ATGGCA

TTGCAT

[38]

PP_0859

Amidohydrolase

CTGGTA

GTGCTT

[36]

edd

Phosphogluconate dehydratase

GTGGCA

TTGTTT

[40]

PP_2836

Fumarylacetoacetate hydrolase family protein

GTGGCT

TTGCAA

[33]

PP_1946

Glucose 1-dehydrogenase

TTGGCA

TTGCAA

[33]

PP_3486

Cytochrome c

ATGGCT

GTGCTT

[40]

PP_1141

ABC transporter substrate-binding protein

TGGGCT

TGGCAT

[40]

ppx

Exopolyphosphatase

ATGGCA

TTGCAT

[42]

PP_3778

Pyrroline-5-carboxylate reductase

TTGACA

TTGCTA

[35]

xdhA

Xanthine dehydrogenase small subunit

TGGGCA

GTGCAT

[37]

Transport

PP_4970

Cytochrome c

GTGGCT

GTGTTT

[40]

ntrB

Nitrogen regulation protein NR(II)

GTGGTT

TTGCAT

[40]

Response to stress

PP_3248

Dyp-type peroxidase

TTGATA

TTGCAA

[38]

PP_3539

MerR family DNA-binding transcriptional regulator

GTGGTT

TTGAGT

[40]

Transcription regulation

PP_2952

LysR family transcriptional regulator

GTGGTT

TGGCAT

[40]

PP_0952

RNAP σ⁵⁴

AAGGCA

TTGCTT

[40]

Uncharacterized

PP_1450

HlpA activation/secretion protein HlpB

GTGGCT

TAGCAT

[40]

Gene	Product	−24 Motifs	−12 Motifs	References
	Flagellar assembly
flgA	Flagellar basal body P-ring formation chaperone FlgA	TCGGCA	TTGCTT	[33, 40]
flgB	Flagellar basal body rod protein FlgB	TTGGCA	TTGCTA	[33, 40]
flgF	Flagellar basal-body rod protein FlgF	TTGGTT	TTGCTT	[33, 40]
flgG	Flagellar basal-body rod protein FlgG	ATGGCT	TTGCAA	[40]
fliE	Flagellar hook-basal body complex protein FliE	CTGGCA	TTGCTT	[33]
motA	Flagellar motor stator protein MotA	TTGGTT	TGGCAT	[34]
	Metabolism
PP_2783	3-oxoacyl-ACP reductase family protein	TGGGCT	TGGCAT	[41]
eutC	Ethanolamine ammonia-lyase subunit EutC	TTGGCA	TTGCAT	[39]
PP_1786	Glycosyltransferase	ATGGCA	TTGCAT	[38]
PP_0859	Amidohydrolase	CTGGTA	GTGCTT	[36]
edd	Phosphogluconate dehydratase	GTGGCA	TTGTTT	[40]
PP_2836	Fumarylacetoacetate hydrolase family protein	GTGGCT	TTGCAA	[33]
PP_1946	Glucose 1-dehydrogenase	TTGGCA	TTGCAA	[33]
PP_3486	Cytochrome c	ATGGCT	GTGCTT	[40]
PP_1141	ABC transporter substrate-binding protein	TGGGCT	TGGCAT	[40]
ppx	Exopolyphosphatase	ATGGCA	TTGCAT	[42]
PP_3778	Pyrroline-5-carboxylate reductase	TTGACA	TTGCTA	[35]
xdhA	Xanthine dehydrogenase small subunit	TGGGCA	GTGCAT	[37]
	Transport
PP_4970	Cytochrome c	GTGGCT	GTGTTT	[40]
ntrB	Nitrogen regulation protein NR(II)	GTGGTT	TTGCAT	[40]
	Response to stress
PP_3248	Dyp-type peroxidase	TTGATA	TTGCAA	[38]
PP_3539	MerR family DNA-binding transcriptional regulator	GTGGTT	TTGAGT	[40]
	Transcription regulation
PP_2952	LysR family transcriptional regulator	GTGGTT	TGGCAT	[40]
PP_0952	RNAP σ⁵⁴	AAGGCA	TTGCTT	[40]
	Uncharacterized
PP_1450	HlpA activation/secretion protein HlpB	GTGGCT	TAGCAT	[40]

Table 1.

Open in new tab

Significant annotation of IVT-generated σ⁵⁴–RNAP binding motifs in the upstream regions of genes involved in various biological processes

Gene	Product	−24 Motifs	−12 Motifs	References
	Flagellar assembly
flgA	Flagellar basal body P-ring formation chaperone FlgA	TCGGCA	TTGCTT	[33, 40]
flgB	Flagellar basal body rod protein FlgB	TTGGCA	TTGCTA	[33, 40]
flgF	Flagellar basal-body rod protein FlgF	TTGGTT	TTGCTT	[33, 40]
flgG	Flagellar basal-body rod protein FlgG	ATGGCT	TTGCAA	[40]
fliE	Flagellar hook-basal body complex protein FliE	CTGGCA	TTGCTT	[33]
motA	Flagellar motor stator protein MotA	TTGGTT	TGGCAT	[34]
	Metabolism
PP_2783	3-oxoacyl-ACP reductase family protein	TGGGCT	TGGCAT	[41]
eutC	Ethanolamine ammonia-lyase subunit EutC	TTGGCA	TTGCAT	[39]
PP_1786	Glycosyltransferase	ATGGCA	TTGCAT	[38]
PP_0859	Amidohydrolase	CTGGTA	GTGCTT	[36]
edd	Phosphogluconate dehydratase	GTGGCA	TTGTTT	[40]
PP_2836	Fumarylacetoacetate hydrolase family protein	GTGGCT	TTGCAA	[33]
PP_1946	Glucose 1-dehydrogenase	TTGGCA	TTGCAA	[33]
PP_3486	Cytochrome c	ATGGCT	GTGCTT	[40]
PP_1141	ABC transporter substrate-binding protein	TGGGCT	TGGCAT	[40]
ppx	Exopolyphosphatase	ATGGCA	TTGCAT	[42]
PP_3778	Pyrroline-5-carboxylate reductase	TTGACA	TTGCTA	[35]
xdhA	Xanthine dehydrogenase small subunit	TGGGCA	GTGCAT	[37]
	Transport
PP_4970	Cytochrome c	GTGGCT	GTGTTT	[40]
ntrB	Nitrogen regulation protein NR(II)	GTGGTT	TTGCAT	[40]
	Response to stress
PP_3248	Dyp-type peroxidase	TTGATA	TTGCAA	[38]
PP_3539	MerR family DNA-binding transcriptional regulator	GTGGTT	TTGAGT	[40]
	Transcription regulation
PP_2952	LysR family transcriptional regulator	GTGGTT	TGGCAT	[40]
PP_0952	RNAP σ⁵⁴	AAGGCA	TTGCTT	[40]
	Uncharacterized
PP_1450	HlpA activation/secretion protein HlpB	GTGGCT	TAGCAT	[40]

Gene	Product	−24 Motifs	−12 Motifs	References
	Flagellar assembly
flgA	Flagellar basal body P-ring formation chaperone FlgA	TCGGCA	TTGCTT	[33, 40]
flgB	Flagellar basal body rod protein FlgB	TTGGCA	TTGCTA	[33, 40]
flgF	Flagellar basal-body rod protein FlgF	TTGGTT	TTGCTT	[33, 40]
flgG	Flagellar basal-body rod protein FlgG	ATGGCT	TTGCAA	[40]
fliE	Flagellar hook-basal body complex protein FliE	CTGGCA	TTGCTT	[33]
motA	Flagellar motor stator protein MotA	TTGGTT	TGGCAT	[34]
	Metabolism
PP_2783	3-oxoacyl-ACP reductase family protein	TGGGCT	TGGCAT	[41]
eutC	Ethanolamine ammonia-lyase subunit EutC	TTGGCA	TTGCAT	[39]
PP_1786	Glycosyltransferase	ATGGCA	TTGCAT	[38]
PP_0859	Amidohydrolase	CTGGTA	GTGCTT	[36]
edd	Phosphogluconate dehydratase	GTGGCA	TTGTTT	[40]
PP_2836	Fumarylacetoacetate hydrolase family protein	GTGGCT	TTGCAA	[33]
PP_1946	Glucose 1-dehydrogenase	TTGGCA	TTGCAA	[33]
PP_3486	Cytochrome c	ATGGCT	GTGCTT	[40]
PP_1141	ABC transporter substrate-binding protein	TGGGCT	TGGCAT	[40]
ppx	Exopolyphosphatase	ATGGCA	TTGCAT	[42]
PP_3778	Pyrroline-5-carboxylate reductase	TTGACA	TTGCTA	[35]
xdhA	Xanthine dehydrogenase small subunit	TGGGCA	GTGCAT	[37]
	Transport
PP_4970	Cytochrome c	GTGGCT	GTGTTT	[40]
ntrB	Nitrogen regulation protein NR(II)	GTGGTT	TTGCAT	[40]
	Response to stress
PP_3248	Dyp-type peroxidase	TTGATA	TTGCAA	[38]
PP_3539	MerR family DNA-binding transcriptional regulator	GTGGTT	TTGAGT	[40]
	Transcription regulation
PP_2952	LysR family transcriptional regulator	GTGGTT	TGGCAT	[40]
PP_0952	RNAP σ⁵⁴	AAGGCA	TTGCTT	[40]
	Uncharacterized
PP_1450	HlpA activation/secretion protein HlpB	GTGGCT	TAGCAT	[40]

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