TABLE 1

Pupylated proteins identified in S. coelicolor

S. coelicolor gene locus	Protein name	Annotation	Detected pupylated peptide(s)^a	Pupylated lysine	Medium^b	Orthologue^c in:				Search engine(s)^d	COG category
S. coelicolor gene locus	Protein name	Annotation	Detected pupylated peptide(s)^a	Pupylated lysine	Medium^b	M. tuberculosis	M. smegmatis	R. erythropolis	C. glutamicum	Search engine(s)^d	COG category
SCO1814	InhA/FabI	Putative enoyl-(acyl carrier protein) reductase	(R)DLGK(+243)QNIR(C)	K177	R	Rv1484	MSMEG_3151	RER_30750	cg2342	MI	I
SCO2090	FtsI	Cell division protein	(K)TGTANRVDPATGK(+243)(Y)	K582	R	Rv2163c	MSMEG_4233	RER_35580	cg2375	M	M
SCO2318		Putative glycosyl transferase	(R)TEHPRAHLVVVGK(+243)(R)	K293	R		MSMEG_6484		cg0481	M	M
SCO2389	AcpP	Acyl carrier protein	(M)AATQEEIVAGLAEIVNEIAGIPVEDVK(+43)LDK(+243)(S)	K31	Y	Rv2244	MSMEG_4326	RER_36730	cg2473	MI	I
SCO2390	FabF	3-Oxoacyl-(acyl carrier protein) synthase II	(R)K(+243)VLGDDVDHM(+16)AVSGTK(S)	K333	R	Rv2246	MSMEG_4328	RER_36740	cg3178	MI	I
SCO2950	HupA	Nucleoid-associated heat-unstable (HU) protein	(K)DADAVLAAFAEVVGDIVSK(+43)GDEK(+243)(V),	K38	Y	Rv2986c	MSMEG_2389			MI	L
		Nucleoid-associated heat-unstable (HU) protein	(K)DADAVLAAFAEVVGDIVSK(+243)GDEK(V)
			(K)DADAVLAAFAEVVGDIVSKGDEK(+243)(V)	K42
SCO3373	ClpC	Clp family ATP-binding protease	(K)IAGVRRDK(+243)(E)	K431	R	Rv3596c	MSMEG_6091	RER_06460	cg3079	M	O
SCO3581		Conserved hypothetical protein	(K)IVNPK(+243)VAGQAEGGR(V)	K134	Y	Rv3688c	MSMEG_6214	RER_04620	cg0335	MI	S
SCO3629	PurA	Adenylosuccinate synthetase	(K)IGTTGRGIGPTYADK(+243)(I)	K139	R	Rv0357c	MSMEG_0759	RER_14280	cg3063	M	F
SCO3878	DnaN	DNA polymerase III, beta chain	(R)EFLWK(+243)PENPDISAVALVPAK(T)	K182	Y	Rv0002	MSMEG_0001	RER_00020	cg0004	MI	L
SCO4296	GroEL2	60-kDa chaperonin 2	(K)VTLGPKGRNVVLEK(+243)(K)	K41	R/Y	Rv3417c	MSMEG_1583	RER_19240	cg3011	M	O
SCO4496		Putative acetyltransferase	(R)FYESC(+57)GYK(+243)EVGRVPGAIR(V)	K147	R/Y					MI	K
SCO4662	Tuf1	Elongation factor Tu-1	(R)TVGAGQVTKINK(+243)(−)	K397	R	Rv0685	MSMEG_1401	RER_17640	cg0587	MI	J
SCO4762	GroEL1	60-kDa chaperonin	(K)DDTTIVDGAGK(+243)RDEVQGR(I)	K338	Y	Rv0440	MSMEG_0880	RER_15260	cg3011	MI	O
			(K)GQGFNAATGEYGDLVK(+243)AGVIDPVK(V)	K490
SCO5032	AhpC	Alkyl hydroperoxide reductase	(K)GKEFQQINHK(+243)TYEGQWK(V)	K31	R/Y	Rv2428	MSMEG_4891	RER_27870	cg2736	MI	O
SCO5679		Putative aldehyde dehydrogenase	(R)EAVDAGAK(+243)LLTGGK(R)	K351	R		MSMEG_2163	RER_44340	cg0067	M	C
SCO5748	OsaA	Putative sensory histidine kinase	(K)GDLSKKITVDAK(+243)(G)	K813	R				cg0483	M	T
SCO6042		Conserved hypothetical protein	(R)AGYADEVQELFDQLAAK(+243)DVTIR(G)	K62	Y	Rv2676c	MSMEG_2782	RER_28490	cg2079	MI	S
SCO7343	HemC1	Porphobilinogen deaminase 1	(R)K(+243)LTDLPR(G)	K113	R	Rv0510	MSMEG_0953	RER_16420	cg0498	MI	H
SCO7442		Putative uncharacterized protein	(K)AVSMSDPNKDTNK(+243)(K)	K22	R					M	S

↵a Amino acid modifications are indicated as follows: +16, oxidation; +57, carbamidomethyl; +43, carbamyl; +243, pupylation.
↵b Y, YEME medium; R, R2YE medium.
↵c Orthologous proteins detected as confirmed pupylated targets in mycobacterial, Rhodococcus, or Corynebacterium pupylomes (10, 11, 19, 25, 50) are underlined. Orthologous proteins identified in these organisms were obtained by a BLAST search through the MAGE genome browser (https://www.genoscope.cns.fr/agc/microscope/home/index.php).
↵d The search engine used was Mascot (M), InSpecT (I), or both (MI).