Extended Data Table 1. Summary of identified phosphosites in various ClpP trapping experiments.

			Experiment 1		Experiment 2
			B. subtilis	wt	B. subtilis	wt	B. subtilis	ΔclpC
Uniprot	Gene Id	Protein Descriptions	control	TRAP	control	TRAP	control	TRAP
Arg-phosphorylated proteins
P71006	albF	Putative zinc protease AlbF		R17
P37941	bfmBAB	2-oxoisovalerate dehydrogenase subunit b				R23
O32222	csoR	Cu-sensing transcriptional repressor CsoR		R24		R24
P37568	ctsR	Transcriptional regulator CtsR		R55		R55		R55
P42416	iolE	Inosose dehydratase		R216
O34645	melA	Alpha-galactosidase		R56		R56
O34338	mntB	Mn transport ATP-binding prot. MntB		R132, (R73)		R132
P16263	odhB	2-oxoglutarate dehydrogenase E2				R300
P12875	rplN	50S ribosomal prot. L14		R17		R17
P42060	rplV	50S ribosomal prot. L22		R11
P12879	rpsH	30S ribosomal prot. S8		R47, R72, R79		R47, R72
P27206	srfAA	Surfactin synthase subunit 1		R226		R226
P33166	tuf	Elongation factor Tu		R384
O34909	yerA	Putative adenine deaminase YerA				R14
O34949	ykoM	Uncharact. HTH-type transcript. regulator YkoM					R89
P42430	ykyB	Uncharacterized prot. YkyB				R26	R26
P54391	ypiF	Uncharacterized prot. YpiF	R4
O07019	yvfU	Uncharact. transcript. regulatory protein YvfU				R143
Phosphorylated proteins, likely pArg
P13800	degU	Transcriptional regulatory prot. DegU				(R184)
P25499	hrcA	Heat-inducible Transcriptional repressor HrcA		(R27)		(R27)
Ser/Thr/Tyr-phosphorylated proteins
P25953	comGA	ComG operon prot. 1						T178
O31461	ilvE	Branched-chain aa transaminase 1	T249
P42956	mtlA	PTS system mannitol-specific EIICB	S365					S365
P55874	rpmI	50S ribosomal prot. L35			S47		S47
P21476	rpsS	30S ribosomal prot. S19			T77
O34607	sdaAA	Probable L-serine dehydratase, α chain						T99
P54334	xkdO	Phage-like element PBSX prot. XkdO					S295
O34833	yceH	Uncharacterized prot. YceH			S296	S296	S296	S296
O32131	yunB	Sporulatio n prot. YunB	T165
P39808	yvyG	Uncharacterized prot. YvyG			Y49	Y49	Y49	Y49
P42294	yxiB	Uncharacterized prot. YxiB				S88