Reaction	Metabolites	Stoichiometry
# Acetylation of proteins
mod_acetyl_c	accoa_c	-1.0
mod_acetyl_c	coa_c	+1.0

# biotin---[acetyl-CoA-carboxylase] ligase
biotin_ligase	atp_c	-1.0
biotin_ligase	btn_c	-1.0
biotin_ligase	amp_c	+1.0
biotin_ligase	ppi_c	+1.0

# Lipoylation (scavenging)
lipoyl_scavenging	lipoate_c	-1.0
lipoyl_scavenging	atp_c	-1.0
lipoyl_scavenging	amp_c	+1.0
lipoyl_scavenging	ppi_c	+1.0

# Lipoylation (de novo synthesis)
lipoyl_denovo	EG50003-MONOMER_mod_pan4p(1)_mod_oc(1)	-1.0
lipoyl_denovo	CPLX0-782_mod_4fe4s(2)	-1.0
lipoyl_denovo	amet_c	-2.0
lipoyl_denovo	nad_c	-1.0
lipoyl_denovo	h_c	-1.0
lipoyl_denovo	EG50003-MONOMER_mod_pan4p(1)	1.0
lipoyl_denovo	CPLX0-782_mod_2fe2s(1)_mod_4fe4s(1)	1.0
lipoyl_denovo	fe2_c	2.0
lipoyl_denovo	met__L_c	2.0
lipoyl_denovo	dad_5_c	2.0
lipoyl_denovo	nadh_c	1.0

# Lipoylation (de novo synthesis using CoA)
lipoyl_denovo_from_coa	occoa_c	-1.0
lipoyl_denovo_from_coa	CPLX0-782_mod_4fe4s(2)	-1.0
lipoyl_denovo_from_coa	amet_c	-2.0
lipoyl_denovo_from_coa	nad_c	-1.0
lipoyl_denovo_from_coa	h_c	-1.0
lipoyl_denovo_from_coa	coa_c	1.0
lipoyl_denovo_from_coa	CPLX0-782_mod_2fe2s(1)_mod_4fe4s(1)	1.0
lipoyl_denovo_from_coa	fe2_c	2.0
lipoyl_denovo_from_coa	met__L_c	2.0
lipoyl_denovo_from_coa	dad_5_c	2.0
lipoyl_denovo_from_coa	nadh_c	1.0

# 2'-(5-triphosphoribosyl)-3'-dephospho-CoA:apo-[citrate (pro-3S)-lyase] 2'-(5-phosphoribosyl)-3'-dephospho-CoA-transferase
citx_transfer_to_citd	2tpr3dpcoa	-1.0
citx_transfer_to_citd	ppi_c	+1.0

# activation of glycyl radical enzymes
gre_activation	FLAVODOXIN1-MONOMER	-1.0
gre_activation	amet_c	-1.0
gre_activation	dad_2_c	1.0
gre_activation	FLAVODOXIN1-MONOMER_mod_Oxidized(1)	1.0
gre_activation	met__L_c	1.0

# CoA-[4'-phosphopantetheine]:apo-[acyl-carrier protein] 4'-pantetheinephosphotransferase
acpP_activation	coa_c	-1.0
acpP_activation	h_c	+1.0
acpP_activation	pap_c	+1.0

# lipid modifications
mod_2nd_pg160_p	pg160_p	-1.0
mod_2nd_pg160_p	2agpg160_p	+1.0
mod_2nd_pe160_p	pe160_p	-1.0
mod_2nd_pe160_p	2agpe160_p	+1.0
mod_1st_pe120_p	pe120_p	-1.0
mod_1st_pe120_p	g3p_c	+1.0
mod_1st_pe140_p	pe140_p	-1.0
mod_1st_pe140_p	g3p_c	+1.0
mod_1st_pe141_p	pe141_p	-1.0
mod_1st_pe141_p	g3p_c	+1.0
mod_1st_pe160_p	pe160_p	-1.0
mod_1st_pe160_p	g3p_c	+1.0
mod_1st_pe161_p	pe161_p	-1.0
mod_1st_pe161_p	g3p_c	+1.0
mod_1st_pe180_p	pe180_p	-1.0
mod_1st_pe180_p	g3p_c	+1.0
mod_1st_pe181_p	pe181_p	-1.0
mod_1st_pe181_p	g3p_c	+1.0
mod_1st_pg120_p	pg120_p	-1.0
mod_1st_pg120_p	g3p_c	+1.0
mod_1st_pg140_p	pg140_p	-1.0
mod_1st_pg140_p	g3p_c	+1.0
mod_1st_pg141_p	pg141_p	-1.0
mod_1st_pg141_p	g3p_c	+1.0
mod_1st_pg160_p	pg160_p	-1.0
mod_1st_pg160_p	g3p_c	+1.0
mod_1st_pg161_p	pg161_p	-1.0
mod_1st_pg161_p	g3p_c	+1.0
mod_1st_pg180_p	pg180_p	-1.0
mod_1st_pg180_p	g3p_c	+1.0
mod_1st_pg181_p	pg181_p	-1.0
mod_1st_pg181_p	g3p_c	+1.0

# Subreactions associated to RNA modifications
# Pseudouridine (isomerization using an aspartate as acceptor/donor in the enzyme)
Y	asp__L_c	0.0

# m7G, m5U, Gm, Cm, Um, m1G, m6A, m2A, m3Y, m5C, m2G, m3U  (Methylation)
m7G,m5U,Gm,Cm,Um,m1G,m6A,m2A,m3Y,m5C,m2G,m3U	amet_c	-1.0
m7G,m5U,Gm,Cm,Um,m1G,m6A,m2A,m3Y,m5C,m2G,m3U	ahcys_c	+1.0

# m4Cm, m62A (Dimethylation)
m4Cm,m62A	amet_c	-2.0
m4Cm,m62A	ahcys_c	+2.0

# D (Reduction (NADPH))
D	nadph_c	-1.0
D	h_c	-1.0
D	nadp_c	+1.0

# t6A (threonylcarbamoyladenylate)
t6A	atp_c	-1.0
t6A	amp_c	+1.0
t6A	ppi_c	+1.0
t6A	hco3_c	-1.0
t6A	h_c	-1.0
t6A	thr__L_c	-1.0
t6A	h2o_c	+1.0

# m6t6A (methylthreonylcarbamoyladenylate)
m6t6A	atp_c	-1.0
m6t6A	amp_c	+1.0
m6t6A	ppi_c	+1.0
m6t6A	hco3_c	-1.0
m6t6A	h_c	-1.0
m6t6A	thr__L_c	-1.0
m6t6A	h2o_c	+1.0
m6t6A	amet_c	-1.0
m6t6A	ahcys_c	+1.0

# i6A (dimethylallylation)
i6A	dmpp_c	-1.0
i6A	ppi_c	+1.0

# acp3U (methylthioadenosine)
acp3U	amet_c	-1.0
acp3U	5mta_c	+1.0

# Q (queuosine: https://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=PWY-6700)
# per PMID 21502530, Cobalamin stimulates activity of QueG, but is not required
Q	preq1_c	-1.0
Q	gua_c	+1.0
Q	amet_c	-1.0
Q	ade_c	+1.0
Q	met__L_c	+1.0
Q	h2o_c	+1.0
Q	RED-THIOREDOXIN-MONOMER	-1.0
Q	RED-THIOREDOXIN-MONOMER_mod_Oxidized(1)	+1.0

# cmo5U
# Changed stoichiometry per PMIDs: 23676670, 25855808, 26681692.
# per PMID 31253794, trhO hydroxylates two adjacent uridines using molecular oxygen
cmo5U	amet_c	-2.0
cmo5U	ahcys_c	2.0
cmo5U	pphn_c	-1.0
cmo5U	h2o_c	1.0
cmo5U	phpyr_c	1.0
cmo5U	o2_c	-1.0

# k2C
k2C	atp_c	-1.0
k2C	amp_c	+1.0
k2C	ppi_c	+1.0
k2C	lys__L_c	-1.0

# I
I	h2o_c	-1.0
I	nh3_c	+1.0

# ac4C (acetylation)
# per PMID 19322199, atp is required for this modification
ac4C	accoa_c	-1.0
ac4C	coa_c	+1.0
ac4C	atp_c	-1.0
ac4C	h2o_c	-1.0
ac4C	adp_c	+1.0
ac4C	pi_c	+1.0

# mnm5U
mnm5U	h2o_c	-2.0
mnm5U	gly_c	-1.0
mnm5U	5fthf_c	-1.0
mnm5U	gtp_c	-1.0
mnm5U	thf_c	+1.0
mnm5U	pi_c	+1.0
mnm5U	gdp_c	+1.0
mnm5U	glx_c	+1.0
mnm5U	amet_c	-1.0
mnm5U	ahcys_c	+1.0

# mnm5s2U (mnm5U + sulfuration: it needs a carrier and a reducer)
mnm5s2U	h2o_c	-2.0
mnm5s2U	gly_c	-1.0
mnm5s2U	5fthf_c	-1.0
mnm5s2U	gtp_c	-1.0
mnm5s2U	thf_c	+1.0
mnm5s2U	pi_c	+1.0
mnm5s2U	gdp_c	+1.0
mnm5s2U	glx_c	+1.0
mnm5s2U	amet_c	-1.0
mnm5s2U	ahcys_c	+1.0
mnm5s2U	atp_c	-1.0
mnm5s2U	amp_c	+1.0
mnm5s2U	ppi_c	+1.0
mnm5s2U	IscS_mod_pydx5p(2)_mod_SH(1)	-1.0
mnm5s2U	IscS_mod_pydx5p(2)	+1.0
mnm5s2U	RED-THIOREDOXIN-MONOMER	-1.0
mnm5s2U	RED-THIOREDOXIN-MONOMER_mod_Oxidized(1)	+1.0

# ms2i6A (sulfuration: it needs a carrier and a reducer)
# per PMID 23543739, grxD is involved in repairing miaB 4fe4s prosthetic group after accepting electron
ms2i6A	dmpp_c	-1.0
ms2i6A	ppi_c	+1.0
ms2i6A	amet_c	-1.0
ms2i6A	ahcys_c	+1.0
ms2i6A	amet_c	-1.0
ms2i6A	met__L_c	+1.0
ms2i6A	dad_5_c	+1.0
ms2i6A	IscS_mod_pydx5p(2)_mod_SH(1)	-1.0
ms2i6A	IscS_mod_pydx5p(2)	+1.0
ms2i6A	CPLX0-7817	-1.0
ms2i6A	CPLX0-7817_mod_Oxidized(1)	+1.0

# s4U, s2C (sulfuration: it needs a carrier ThiI)
# per PMID 24914049, the 4fe4s prosthetic group in YdaO helps donate sulfur, and an additional ferredoxin is not required
# per PMID 10753862, mechanism does not require thioredoxin or other reducing equivalent
s4U,s2C	atp_c	-1.0
s4U,s2C	amp_c	+1.0
s4U,s2C	ppi_c	+1.0
s4U,s2C	IscS_mod_pydx5p(2)_mod_SH(1)	-1.0
s4U,s2C	IscS_mod_pydx5p(2)	+1.0
