Table 1.

Known protein-encoding genes related to fundamental biological processes in M. maripaludis S2

Biological process	Subprocess*	Possibly essential†	Unassigned†	Nonessential†
Energy metabolism	Methanogenesis (32)	mer, mch, fwdHFGDAC, mcrBDCGA, mtrEDCBAGH, or900, ftr, atwA	fwdB	hmd, fmdE1, mtd, fmdE2ACB1B2
	ATP generation (9)	atpHIKECFABD
	Membrane-bound hydrogenases (34)	ehaABCDEFGHIJKLMNOT	ehbQ, ehbJ, 1626, ehbF	ehaPQRS, ehbCD, ehbN, ehbA, ehbOMLK, ehbG, ehbE
	Cytoplasmic hydrogenases (17)	frcD, vhuUAGD,	vhuB	frcBG, frcA, vhcDGAB, fruADGB
Replication	DNA polymerases (3)	DP1, DP2		polB
	Replication factors (23)	priL, mcm1, priS, rfcB, rfcA, rpa2, topA, lig, top6B, rpa1, pcnA, top6A, pcnA gins15	rnhA	mcm2, mcm3, mcm4, rpa3, dnaG, fen1, rnhB, smc1
Transcription	RNA polymerase (12)	rpoP, rpoL, rpoE’, rpoD,rpoN, rpoK, rpoHB2B1A1A2	rpoF
	Transcription factors (8)	tfe, tfb, tbp, nusA, nusG	1015, spt4	tfs
Translation	tRNA synthetase and related proteins (26)	0212,0255, tyrS, metS, alaS, thrS, valS, 0688, proS, leuS, serS, gltX, argS, pheT, lysS, ileS, pheS, trpS, hisS, aspS		0002, truA, 0377, 0693, 0816, cysS
	Ribosomal proteins (60)	rplX, rpl31e, rpl40e, rpl37ae, rpl12p, rpl1P, rps17E, rpl34e, rpl24e, rps28e, rpl7ae, rps2P, rps3ae rps6e, rpl10e, rps13p, rps4p, rps11p, rpl18e, rpl13p, rps9p, rps12p, rps7p, rps10p, rpl22p, rps3p, rpmC, rps17p, rpl14p, rpl24p, rps4e, rpl5p, rps14p, rps8p, rpl6p, rpl32e, rpl19e, rpl18p, rps5p, rpl30p, rpl15p, rpl3p, rpl4p, rplW, rpl2p, rps19p, rps15p, rps8e, rpl44e	rpl21e, rps19e, rplP0, rpl15, rps24e, rps27ae, rpl37e, rpl30e, rpl11p, rps27e	rpl39e
	Translation factors (14)	aIF6, infB, aIF2β, aIF1A, aIF5A, 1131, aIF2γ, aEF2,selB, aEF1α, aEF1β	aIF2α	0738, aIF2BI

*The number in parentheses corresponds to the total number of known genes for that specific subprocess.

^†Genome annotation code number (MMP#) is used for genes that do not possess a gene symbol. Gene names are defined in Dataset S4.