Table 2.

Metabolite and reaction input for the network shown in figure 1. (Metabolite abbreviations are the usual in biochemistry, except for pal (palmitoyl CoA), peta (phosphatidylethanolamine), pser (phosphatidylserine), mthf (5,10-methylene-tetrahydrofolate). Input fluxes (for k source substrate) and output fluxes (for k sink product) are indicated by Jik and Jok, respectively. For redox coenzyme NAD⁺/NADH, a reversible flux Jk is defined. Reversible and irreversible reactions are indicated, in the reaction equations, by the symbols ↔ and →, respectively. Last column shows the corresponding Mycoplasma genitalium genes considered as essential by Glass et al. (2006). The four cases in boldface correspond to non-essential genes. n.i., non-identified in M. genitalium. Input file for Metatool is available upon request to the corresponding author.)

external metabolites		internal metabolites
metabolite input
sources: glc (Ji1), pal (Ji2), ade (Ji3), gua (Ji4), ura (Ji5), ser (Ji6), p (Ji7), nadh (Jk1), nad (Jk2) sinks: lac (Jo1), peta (Jo2), atp (Jo3), ctp (Jo4), gtp (Jo5), utp (Jo6), datp (Jo7), dctp (Jo8), dgtp (Jo9), ttp (Jo10), gly (Jo11)		g6p, f6p, fbp, gdp, dhp, bpg, 3pg, 2pg, pep, pyr, g3p, mag, dag, cdp-dag, pser, sbp, s7p, rip, xip, e4p, rup, prpp, amp, gmp, cmp, ump, tmp, adp, gdp, cdp, udp, dump, dadp, dgdp, dcdp, dudp, dutp, tdp, mthf, dhf, thf, pp

EC	name	abbreviation	input reaction equations	Glass et al. (2006)
enzyme and reaction input
2.7.1.69	phosphotransferase system	PTS	glc+pep→g6p+pyr	MG041, 069, 429
5.3.1.9	glucose-6-phosphate isomerase	PGI	g6p↔f6p	MG111
2.7.1.11	6-phosphofructokinase	PFK	f6p+atp →fbp+adp	MG215
4.1.2.13	fructose-1,6-bisphosphate aldolase	FBA	fbp↔gdp+dhp	MG023
5.3.1.1	triose-phosphate isomerase	TPI	gdp↔dhp	MG431
1.2.1.12	glyceraldehyde-3-phosphate dehydrogenase	GAP	gdp+nad+p↔bpg+nadh	MG301
2.7.2.3	phosphoglycerate kinase	PGK	bpg+adp↔3pg+atp	MG300
5.4.2.1	phosphoglycerate mutase	GPM	3pg↔2pg	MG430
4.2.1.11	enolase	ENO	2pg↔pep	MG407
2.7.1.40	pyruvate kinase	PYK	pep+adp→pyr+atp	MG216
1.1.1.27	lactate dehydrogenase	LDH	pyr+nadh↔lac+nad	MG460
1.1.1.94	sn-glycerol-3-phosphate dehydrogenase	GPS	dhp+nadh→g3p+nad	n.i.a
2.3.1.15	sn-glycerol-3-phosphate acyltransferase	PLSb	g3p+pal→mag	n.i.
2.3.1.51	1-acyl-sn-glycerol-3-phosphate acyltransferase	PLSc	mag+pal→dag	MG212
2.7.7.41	phosphatidate cytidyltransferase	CDS	dag+ctp→cdp-dag+pp	MG437
2.7.8.8	phosphatidylserine synthase	PSS	cdp-dag+ser→pser+cmp	n.i.
4.1.1.65	phosphatidylserine decarboxylase	PSD	pser→peta	n.i.
4.1.2.13	fructose-1,6-bisphosphate aldolase	FBA2	gdp+e4p↔sbp	MG023
3.1.3.37b	sedoheptulose-1,7-bisphosphatase	SPH	sbp→s7p+p	n.i.
2.2.1.1	transketolase	TKT	gdp+s7p↔rip+xip	MG066
2.2.1.1	transketolase	TKT2	e4p+xip↔f6p+gdp	MG066
5.1.3.1	ribulose-phosphate 3-epimerase	RPE	xip↔rup	MG112
5.3.1.6	ribose-5-phosphate isomerase	RPI	rup↔rip	MG396
2.7.6.1	phosphoribosylpyrophosphate synthase	PRS	rip+atp→prpp+amp	MG058
2.4.2.8	hypoxanthine phosphoribosyltransferase	HPT	prpp+ade→amp+pp	MG276
2.4.2.8	hypoxanthine phosphoribosyltransferase	HPT2	prpp+gua→gmp+pp	MG458
2.4.2.9	uracil phosphoribosyltransferase	UPP	prpp+ura→ump+pp	MG030
3.6.1.1	inorganic pyrophosphatase	PPA	pp→2p	MG351
2.7.4.3	adenylate kinase	ADK	amp+atp→2adp	MG171
2.7.4.8	guanylate kinase	GMK	gmp+atp→gdp+adp	MG107
2.7.4.14b	cytidylate kinase	CMK	ump+atp→udp+adp	MG330
2.7.4.14	cytidylate kinase	CMK2	cmp+atp→cdp+adp	MG330
2.7.4.6	nucleoside diphosphate kinase	NDK	gdp+atp↔gtp+adp	MG216c
2.7.4.6	nucleoside diphosphate kinase	NDK2	udp+atp↔utp+adp	d
2.7.4.6	nucleoside diphosphate kinase	NDK3	dadp+atp↔datp+adp	MG216c
2.7.4.6	nucleoside diphosphate kinase	NDK4	dgdp+atp↔dgtp+adp	MG216c
2.7.4.6	nucleoside diphosphate kinase	NDK5	ctp+adp↔cdp+atp	d
2.7.4.6	nucleoside diphosphate kinase	NDK6	dcdp+atp↔dctp+adp	d
2.7.4.6	nucleoside diphosphate kinase	NDK7	dutp+adp↔dudp+atp	d
2.7.4.6	nucleoside diphosphate kinase	NDK8	tdp+adp↔ttp+adp	MG034
1.17.4.1	ribonucleoside diphosphate reductase	NRD	adp+nadh→dadp+nad	MG229–MG231
1.17.4.1	ribonucleoside diphosphate reductase	NRD2	gdp+nadh→dgdp+nad	MG229–MG231
1.17.4.1	ribonucleoside diphosphate reductase	NRD3	cdp+nadh→dcdp+nad	MG229–MG231
6.3.4.2	CTP synthase	PYR	utp→ctp	n.i.
3.5.4.13	dCTP deaminase	DCD	dctp→dutp	n.i.
2.7.4.9	thymidylate kinase	TMK	dudp+adp↔dump+atp	MG006
2.7.4.9	thymidylate kinase	TMK2	tmp+atp↔tdp+adp	MG006
2.1.1.45	thymidylate synthase	THY	dump+mthf→dhf+tmp	MG227
1.5.1.3	dihydrofolate reductase	DFR	dhf+nadh↔thf+nad	MG228
2.1.2.1	glycine hydroxymethyltransferase	GHT	ser+thf↔gly+mthf	MG394

^aMG039 codes for a non-essential FAD-dependent glycerol-3-phosphate dehydrogenase.

^bSedoheptulose-1,7-bisphosphatase and cytidylate kinase are missing in table 1 of Gil et al. (2004).

^cMG216 encodes pyruvate kinase. This glycolytic enzyme can also catalyse the phosphorylation of purine dinucleotides using PEP as a phosphate donor.

^dMushegian & Koonin (1996) proposed MG264 (dephospho-CoA kinase, EC 2.7.1.24) and MG268 (conserved hypothetical protein) as candidates for the role of NDK. Both genes are independently dispensable after Glass et al. (2006).