Table 1. Compounds Tested To Validate TFBMiner^a.

ligand	KEGG compound ID	source	regulator	identified chains	identified biosensors	reference
original biosensor was identified
β-l-arabinose	C02479	E. coli	AraC	3	2095	(18)
l-arginine	C00062	B. licheniformis	RocR	994	10,828	(19)
benzoate	C00180	A. baylyi	BenM	70	2488	(20)
benzoate	C00180	C. necator	BenM	70	2488	(9)
glutarate	C00489	P. putida	CsiR	33	435	(21)
l-kynurenine	C00328	C. necator	KynR	558	2688	(9)
l-phenylalanine	C00079	C. necator	PhhR	1175	1955	(9)
l-phenylalanine	C00079	P. aeruginosa	PhhR	1175	1955	(22)
phenylglyoxylate	C02137	C. necator	PhgR	25	367	(9)
l-proline	C00148	R. leguminosarum	PutR	159	6480	(23)
salicylate	C00805	C. necator	NahR	84	380	(9)
tartrate	C00898	C. necator	TtdR	273	8523	(9)
l-tyrosine	C00082	C. necator	HpdA	1140	11,622	(9)
vanillate	C06672	C. crescentus	VanR	305	505	(24)
xanthine	C00385	C. necator	XdhR	12	3131	(9)
d-xylose	C00181	P. megaterium	XylR	19	8307	(25)
original biosensor was not identified: resemblance of the ligand’s structure to that of the original inducer molecule
ε-caprolactam	C06593	Acinetobacter sp. NCIMB 9871	ChnR	0	0	(26)
isoprene	C16521	R. pickettii	TbuT	0	0	(27)
original biosensor was not identified: operon regulation is unrelated to ligand metabolism
N-(3-oxohexanoyl)-l-homoserine lactone	C21198	V. fischeri	LuxR	0	0	(28)
naringenin	C00509	P. putida	TtgR	114	0	(29)
original biosensor was not identified: the KEGG database is incomplete (compounds listed as products rather than substrates; gene entries not linked to entries for enzymes or organisms; strains or enzymes not listed)
3-hydroxypropanoate	C01013	C. necator	HpdR	68	14	(30)
β-alanine	C00099	C. necator	OapR	213	2904	(9)
cyclohexane-1-carboxylate	C09822	C. necator	BadR	0	0	(9)
glutarate	C00489	P. putida	GcdR	33	435	(21)
l-isoleucine	C00407	P. putida	BkdR	110	955	(31)
naringenin	C00509	H. seropedicae	FdeR	114	0	(32)
progesterone	C00410	P. simplex	SRTF1	52	0	(33)
sulfoacetate	C14179	C. necator	SauR	0	0	(9)
original biosensor was not identified: gene organization does not match the required model
acetoin	C00466	C. necator	AcoR	28	0	(9)
acrylate	C00511	R. sphaeroides	AcuR	2	150	(34)
choline	C00114	E. coli	BetI	363	2894	(35)
erythromycin A	C01912	E. coli	MphR	0	0	(36)
glucarate	C00818	E. coli	CdaR	22	1159	(37)
oleate	C00712	E. coli	FadR	32	0	(38)
l-phenylalanine	C00079	E. coli	TyrR	1175	1955	(39)
putrescine	C00134	E. coli	PuuR	362	1319	(40)
l-tyrosine	C00082	E. coli	TyrR	1140	11,622	(39)

^aThe most frequent issues that result in the tool’s inability to find the reported biosensors are outlined.