Table 1.

List of COGs and E. coli Gene Designations by Groups

Group^a	COG number^b	E. coli gene designation^b
1	0048, 0049, 0051, 0052, 0096, 0098, 0099, 0100^c, 0103, 0184^c, 0185^c, 0186, 0199^c, 0522, 0080^c, 0081, 0087, 0088, 0089^c, 0090^c, 0091, 0093, 0094, 0097, 0102, 0197, 0198^c, 0244, 0256^c, [0050], [0231], 0361, [0480], 0532	rpsL, rpsG, rpsJ, rpsB, rpsH, rpsE, rpsM, rpsK, rpsI, rpsO, rpsS, rpsQ, rpsN, rpsD, rplK, rplA, rplC, rplD, rplW, rplB, rplV, rplN, rplE, rplF, rplM, rplP, rplX, rplJ, rplR, [tufB, cysN, tufA, selB], [yeiP, efp], infA, [fusA, prfC], infB
2	0006^d, 0024, 0112^d, 0201, 0541, 0552	[pepP, pepQ, ec1788728], map, glyA, secY, ffh, ftsY
3	0085, 0086, 0180, 0202, 0250, 0258, 0468^d, 0592	rpoB, rpoC, trpS, rpoA, [nusG, rfaH], [exo, polA_1], recA, dnaN
4	0012, [0037]	ychF, [mesJ, ydaO]
5	[0008^f], 0013^g, 0016^f, 0018^f, 0030^g, 0060^f, 0072^f, 0092^e ^g, 0101^e ^g, 0124^g, 0125^g, 0143^f, 0162^f, 0172^f, 0200^e ^f 0255^e ^g, 0441^f, 0442^f, 0459^d ^f, 0470^f, [0492^e ^f], 0495^f, 0525^g, 0533^g, [0550^g], [0575^d ^g], 0636^e ^g, [1109^f]	[glnS, yadB, gltX], alaS, pheS, argS, ksgA, ileS, pheT_2, rpsC, truA, hisS, tmk, metG_1, tyrS, serS, rplO, rpmC, thrS, proS, groL, holB, [trxB, ahpF], leuS, valS, ygjD, [topA_1, topB], [cdsA, ec1787677], atpE, [cpsG, mrsA]
6	[0073], [0526]	[pheT_1, ygiH, metG_2], [trxA, yfiG, dsbD, yejO, ybbN, dsbA]

Group 1: rproteins and translation factors; 2: ribosome associated proteins; 3: transcription and replication proteins; 4: proteins of unknown function; 5: proteins that do not exhibit 3 domain phylogeny; and 6: protein families.

Square brackets are used to show COGs that contain more than one E. coli ORF.

COGs for ribosomal proteins that show the Archaea to be polyphyletic, but both the Bacteria and Eucarya are strongly supported monophyletic groups.

These COGS are missing an ORF for a single bacterium that contains a highly reduced genome and therefore are included in this analysis.

Additional non-three-domain COGs that are missing from a single genome analyzed.

Non-three-domain COGs with statistically supported lateral gene transfers.

Non-three-domain COGs with no statistical support for lateral gene transfers.