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 |