Table 2. Genes modeled in the metabolic reconstruction.

The ‘MMSYN1_’ prefix on the locus tags has been omitted for brevity. The reaction column provides the specific reaction name or general description of the gene (if involved in multiple reactions). Reaction names may appear multiple times if there are multiple gene products that can catalyze that reaction. Column Ess_Tn5 contains a $\cdot$ if the gene is non-essential, a $\mathrm{\square }$ if it is quasi-essential, or a ■ if it has been determined to be essential through the transposon mutagenesis experiments. A dagger in this column indicates that the automatic essentiality assignment required manual intervention. Column Ess_FBA contains a $\cdot$ if the gene is non-essential or a ■ if it has been determined to be essential through FBA. Loci marked with an asterisk are genes that are non-essential only ‘technically’ with respect to FBA (see Section 'In silico gene knockouts and mapping to in vivo essentiality'). The doubling times predicted by FBA for non-essential genes were all 2.02 hr, with the exception of single knockouts of loci pdhC/0227 through ackA/0230, which all had doubling times of 3.22 hr; locus punA/0747 with a doubling time of 2.04 hr; and locus gltP/0886 with a doubling time of 2.03 hr.

Locus	Reaction	EssTn5	EssFBA	Locus	Reaction	EssTn5	EssFBA	Locus	Reaction	EssTn5	EssFBA
Amino acid metabolism				Cofactor metabolism				0798	UPPRT	■	■
0381*	AHCi	$\cdot$	$\cdot$	0823	5FTHFPGS	$\mathrm{\square }$	■	0330	dAdn kinase 1	$\cdot$	$\cdot$
0163	ALATRS	■	■	0390	FMETTRS	$\mathrm{\square }$	■	0382	dAdn kinase 2	$\cdot$	$\cdot$
0535	ARGTRS	■	■	0291	FMNAT	■	■	Transport
0076	ASNTRS	■	■	0443	FTHFCL	■	■	0822	5FTHFabc	$\mathrm{\square }$	■
0287	ASPTRS	■	■	0799	GHMT	$\mathrm{\square }$	■	0876	AA permease 1	$\cdot$	$\cdot$
0837	CYSTRS	■	■	0684	MTHFC	$\mathrm{\square }$	■	0878	AA permease 2	$\mathrm{\square }$	$\cdot$
0687	GLNTRAT	■	■	0259	NADK	■	■	0789	ATPase	■†	■
0688	GLNTRAT	■	■	0378	NADS	■	■	0790	ATPase	■	■
0689	GLNTRAT	■	■	0614	NCTPPRT	■	■	0791	ATPase	■	■
0126	GLUTRS_Gln	■	■	0380	NNATr	■	■	0792	ATPase	■	■
0405	GLYTRS	■	■	Lipid metabolism				0793	ATPase	■	■
0288	HISTRS	■	■	0621	ACP	■	■	0794	ATPase	■	■
0519	ILETRS	■	■	0419	ACPPAT	■	■	0795	ATPase	■	■
0634	LEUTRS	■	■	0513	ACPS	■	■	0796	ATPase	■	■
0064	LYSTRS	■	■	0512	AGPAT	■	■	0879	CA2abc	■	■
0432${}^{\mathrm{\ast }}$	MAT	■	$\cdot$	0117	APG3PAT	■	■	0836	COAabc	■	■
0012	METTRS	■	■	0139	BPNT	$\mathrm{\square }$	■	0642	EcfA	■	■
0528	PHETRS	■	■	0147	CLPNS	■	■	0643	EcfA	■	■
0529	PHETRS	■	■	0697	DAGGALT	$\mathrm{\square }$	$\cdot$	0641	EcfT	■	■
0282	PROTRS	■	■	0114	DAGPST/DAGGALT	■	■	0233	GLCpts	■	■
0133	Peptidase 1	$\cdot$	$\cdot$	0304	DASYN	■	■	0234	GLCpts	■	■
0305	Peptidase 2	$\mathrm{\square }$	$\cdot$	0420	FAKr	■	■	0694	GLCpts	■	■
0444	Peptidase 3	$\mathrm{\square }$	$\cdot$	0616	FAKr	■	■	0779	GLCpts	■	■
0479	Peptidase 4	$\mathrm{\square }$	$\cdot$	0617	FAKr	$\mathrm{\square }$	■	0886	GltP	$\mathrm{\square }$	$\cdot$
0061	SERTRS	■	■	0115	GALU	■	■	0685	Kt6	■	■
0222	THRTRS	■	■	0218	GLYK	■	■	0686	Kt6	■	■
0308	TRPTRS	■	■	0733	PGMT/PPM	■	■	0401	LIPTA	$\cdot$	$\cdot$
0613	TYRTRS	■	■	0214	PGPP	$\mathrm{\square }$	■	0787	MG2abc	■	■
0260	VALTRS	■	■	0875	PGSA	■	■	0314	NACabc	■	■
Central metabolism				0113	PSSYN	■	■	0165	Opp	$\mathrm{\square }$	$\cdot$
0230	ACKr	■	$\cdot$	0813	UDPG4E	■	■	0166	Opp	$\mathrm{\square }$	$\cdot$
0493	AGDC	$\mathrm{\square }$	$\cdot$	0814	UDPGALM	■	■	0167	Opp	$\mathrm{\square }$	$\cdot$
0495	AMANK	$\cdot$	$\cdot$	Macromolecules				0168	Opp	$\mathrm{\square }$	$\cdot$
0494	AMANPEr	$\cdot$	$\cdot$	0394	Lon	$\mathrm{\square }$	■	0169	Opp	$\mathrm{\square }$	$\cdot$
0732	DRPA	$\cdot$	$\cdot$	0650	Met peptidase	■	■	0345	P5Pabc	■	■
0213	ENO	■	■	0201	Pept. deformylase	■	■	0425	PIabc	■	■
0131	FBA	■	■	Nucleotide metabolism				0426	PIabc	■	■
0726	G6PDA	$\cdot$	$\cdot$	0651	(D)ADK	■	■	0427	PIabc	■	■
0607	GAPD	■	■	0413	ADPT	■	■	0877	RIBFLVabc	■	■
0451	GAPDP	■	$\cdot$	0129	CTPS	■	■	0008	RNS	■	■
0475	LDH_L	■	$\cdot$	0347	CYTK	$\mathrm{\square }$	■	0009	RNS	■	■
0435	MAN6PI	$\cdot$	$\cdot$	0515	DCMPDA	$\mathrm{\square }$	$\cdot$	0010	RNS	■	■
0227	PDH_E2/_acald	$\cdot$	$\cdot$	0447	DUTPDP	■	■	0011	RNS	■	■
0228	PDH_E3	$\cdot$	$\cdot$	0203	GK	■	■	0195	SPRMabc	$\mathrm{\square }$	■
0220	PFK	■	■	0216	GUAPRT	$\mathrm{\square }$	■	0196	SPRMabc	$\mathrm{\square }$	■
0445	PGI	■	■	0747	PNP	$\mathrm{\square }$	$\cdot$	0197	SPRMabc	$\mathrm{\square }$	■
0606	PGK	■	■	0344	PPA	■	■	0706	THMPPabc	$\mathrm{\square }$	■
0729	PGM	■	■	0771	RNDR	$\mathrm{\square }$	■	0707	THMPPabc	$\mathrm{\square }$	■
0831	PRPPS	■	■	0772	RNDR	■	■	0708	THMPPabc	$\mathrm{\square }$	■
0229	PTAr	■	$\cdot$	0773	RNDR	$\mathrm{\square }$	■
0221	PYK	■	■	0140	TMDK1/DURIK1	■	■
0262	RPE	$\mathrm{\square }$	■	0045	TMPK	■	■
0800	RPI	$\mathrm{\square }$	■	0065	TRDR	■	■
0316	TKT	$\mathrm{\square }$	■	0819	TRDR	■	■
0727	TPI	■	■	0537	UMPK	■	■