Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

Table 1 Summary of results obtained by Function Discovery V1.0 when applied to ten known-function TRs

TR^a	Pathway name	Known pathway genes	Genes clustered with the TR^b	TRE	Ref
betI (B1590)	glycine betaine synthesis	betABTI	betABTI	choline	[21]
catR (A2107)	benzoate degradation	catABCR	catABCR	cis, cis-muconate	[22]
cymR (A3550)	p-cumate catabolism	cymAaAbAcAdBCDEFHG	cymAaAbAcAd─CDE─ ─ ─	p-cumate	[23]
cysB (A2466)	sulfur metabolism	cysABPTWA	cysABPTW	N-acetyl-serine	[24]
glpR (A0643)	glycerol metabolism	glpABCDKFR	glp─ ─ ─DKFR	glycerol-3-phosphate	[25]
hpaR (B2027)	hydroxyphenylacetate catabolism	hpaGEDFHIR	hpaGEDFHIR	4-hydroxy-phenylacetate	[26]
kynR (A0736)	oxidative tryptophan degradation	kynABU	kynABU	L-kynurenine	[27]
hutC (A2946)	histidine degradation	hutHUIFGC	hutHUIFGC	urocanate	[28, 29]
rcoM (A2142)	carbon monoxide oxidation	coxBCMSLDEFGHIK	cox ─ ─SMLDE ─G ─ ─ ─	carbon monoxide	[30]
modEB2851)	molybdate transport	modABCDE	modABC─E	molybdenum	[31]

^aTranscriptional regulators of interest, the locus tag of the gene is in parentheses and excludes the “bxe_” prefix.
^bGenes missing in the cluster are identified by a dash (─). This table summarizes the analysis of 10 genes upstream and 10 genes downstream of the TR of interest.

ISSN: 1471-2164