Table 3.

Motif discovery for the clustering genes

Cluster	Genes or operons for motif discovery	Strict consensus of known TF-like box (See also Figure 4)	Hits of consensus
Cluster I	rps-rpm-rpl operon, rpsLG, rpsF-priB-rpsR-rplI, purEK, ruvCAB, rpsB, rplMI, rpsP-rimM-trmD-rplS, nusA-infB and rluC	PurR-like box: 5' ACGCAATCGTTTTCNT 3'	rps-rpm-rpl operon, purEK, ruvCAB, rpsB, rpsP-rimM-trmD-rplS, nusA-infB and rluC
Cluster II	hmuRSTUV, YPO0682, YPO0778, YPO0988, YPO1003, YPO1011, ysuFJIHG, YPO1735, YPO1854-YPO1856, irp2-irp1-ybtUTE, ybtPQXS, YPO2163, sufABCDSE, yfeABCD, nrdHIEF, yfuABC, YPO3086, YPO3339, yacK, yhhN-zntA and YPO4022	Fur-like box: 5' TGATAATGATTATCATTATCA 3'	hmuRSTUV, YPO0682, YPO0988, YPO1011, ysuFJIHG, YPO1735, YPO1854-YPO1856, irp2-irp1-ybtUTE, YPO2163, sufABCDSE, yfeABCD, nrdHIEF, yfuABC, YPO3086, YPO3339, yacK, yhhN-zntA and YPO4022
Cluster III	cysB, ssuEADCB, cysK, YPO3541, YPO1517-YPO1516, YPO1316, YPO1317-YPO1319, fliY, sbp1, tauABCD, YPO0186, YPO2360, YPO3010, cysP, YPO4112, YPO4108, ilvC, YPO2315 and gntT	Fnr-like box: 5' TGAN6TCAA 3'	ssuEADCB, cysK, YPO1517-YPO1516, YPO1317-YPO1319, fliY, sbp1, tauABCD and gntT
Cluster IV	sdhCDAB-sucABCD, nuoA-N, cyoABCDE, purB, pta, kbl-tdh, metG, aceE, cysJIH, acnB, murEFXD, YPO1523, gph, trpS, pepD, accBC, mutS, ppc, cydAB, fadBA, fadL, fumA, mdh, oppABCDF, treBC, manX, napFDABC and frdABCD	Fnr/Crp-like box: 5' TGANNNNNNTCA 3' ArcA-like box:5' GTTAATTAATGT 3'	sdhCDAB-sucABCD, pta, kbl-tdh, gph, pepD, mutS, cydAB, fadBA, fumA, oppABCDF, treBC, manX and frdABCD acnB, pepD, mutS, mdh, oppABCDF, manX and frdABCD