Table 2 Functional investigation of modules identified.
index | Operons included | Biological function description |
|---|---|---|
1 | aceBAK, acs, adhE, fruBKA, fruR, icdA, iclMR, mlc, ppsA, ptsG, ptsHI_crr, pykF | Hexose PTS transport system, PEP generation, Acetate usage, glyoxylate shunt |
2 | acnA, fpr, fumC, marRAB, nfo, sodA, soxR, soxS, zwf | Oxidative stress response |
3 | ada_alkB, aidB, alkA, ahpCF, dps, gorA, katG, oxyR | Oxidative stress response, Alkylation |
4 | alaWX, aldB, argU, argW, argX_hisR_leuT_proM, aspV, dnaA, leuQPV, leuX, lysT_valT_lysW, metT_leuW_glnUW_metU_glnVX, metY_yhbC_nusA_infB, nrdAB, pdhR_aceEF_lpdA, pheU, pheV, proK, proL, proP, sdhCDAB_b0725_sucABCD, serT, serX, thrU_tyrU_glyT_thrT, thrW, tyrTV, valUXY_lysV, yhdG_fis | rRNA, tRNA genes, DNA synthesis system, pyruvate dehydrogenase and ketoglutarate dehydrogenase system |
5 | araBAD, araC, araE, araFGH, araJ | Arabinose uptake and usage |
6 | argCBH, argD, argE, argF, argI, argR, carAB | Arginine usage, urea cycle |
7 | caiF, caiTABCDE, fixABCX | Carnitine usage |
8 | clpP, dnaKJ, grpE, hflB, htpG, htpY, ibpAB, lon, mopA, mopB, rpoH | Heat shock response |
9 | codBA, cvpA_purF_ubiX, glnB, glyA, guaBA, metA, metH, metR, prsA, purC, purEK, purHD, purL, purMN, purR, pyrC, pyrD, speA, ycfC_purB, metC, metF, metJ | Purine synthesis, purine and pyrimidine salvage pathway, methionine synthesis |
10 | cpxAR, cpxP, dsbA, ecfI, htrA, motABcheAW, ppiA, skp_lpxDA_fabZ, tsr, xprB_dsbC_recJ | Stress response, Conjugative plasmid expression, cell motility and Chemotaxis |
11 | dctA, dcuB_fumB, frdABCD, yjdHG | C4 dicarboxylate uptake |
12 | edd_eda, gntKU, gntR, gntT | Gluconate usage, ED pathway |
13 | csgBA, csgDEFG, envY_ompT, evgA, gcvA, gcvR, gcvTHP, gltBDF, ilvIH, kbl_tdh, livJ, livKHMGF, lrp, lysU, ompC, ompF, oppABCDF, osmC, sdaA, serA, stpA | Amino acid uptake and usage |
14 | fdhF, fhlA, hycABCDEFGH, hypABCDE | Formate hydrogenlyase system |
15 | flgAMN, flgBCDEFGHIJ, flgKL, flgMN, flhBAE, flhDC, fliAZY, fliC, fliDST, fliE, fliFGHIJK, fliLMNOPQR, tarTapcheRBYZ | Flagella motility system |
16 | ftsQAZ, rcsAB, wza_wzb_b2060_wcaA_wcaB | Capsule synthesis, cell division |
17 | gdhA, glnALG, glnHPQ, nac, putAP | Glutamine and proline utilization |
18 | glmUS, manXYZ, nagBACD, nagE | Glucosamine, mannose utilization |
19 | glpACB, glpD, glpFK, glpR, glpTQ | Glycerol phosphate utilization |
20 | lysA, lysR, tdcABCDEFG, tdcR | Serine, threonine usage |
21 | malEFG, malK_lamB_malM, malPQ, malS, malT, malZ | Maltose utilization |
22 | rhaBAD, rhaSR, rhaT | Rhamnose utilization |
23 | appCBA, appY, betIBA, betT, cydAB, cyoABCDE, fadBA, focA_pflB, fumA, glcC, glcDEFGB, gltA, lctPRD, mdh, nuoABCEFGHIJKLMN, fabA, fadL, fadR, uspA | Oxidative phosphorylation, Glycolate, lactose utilization, fatty acid degradation |
24 | cytR, deoCABD, deoR, nupC, nupG, tsx, udp | Nucleosides uptake and usage |
25 | cirA, entCEBA, fecABCDE, fecIR, fepA_entD, fepB, fepDGC, fhuACDB, fur, tonB | Iron uptake system |
26 | galETKM, galR, galS, mglBAC | Galactose uptake and usage |
27 | dmsABC, fdnGHI, narGHJI, narK, nirBDC_cysG, nrfABCDEFG, torCAD, torR | Nitrogen metabolism, Nitrate and nitrite reductase, |
28 | narZYWV, nhaA, nhaR, osmY | intracellular pH regulation |
29 | aslB, inaA, mdlA, rob, ybaO, ybiS, yfhD | Stress response |
30 | cutC, dapA_nlpB_purA, ecfABC, ecfD, ecfF, ecfG, ecfH, ecfJ, ecfK, ecfLM, fkpA, ksgA_epaG_epaH, lpxDA_fabZ, mdoGH, nlpB_purA, ostA_surA_pdxA, rfaDFCL, rfbO, rpoE_rseABC, uppS_cdsA_ecfE | RpoE regulated stress response, lipopolysaccharide synthesis |
31 | ansB, cpdB, cyaA, dadAX, epd_pgk, glgCAP, glgS, ivbL_ilvBN, ompA, speC, srlAEBD_gutM_srlR_gutQ, tnaLAB, ubiG, yhfA | Sorbitol and Glycogen metabolism |
32 | atoC, atoB, hydHG, hypA, pspABCDE, pspF, rtcAB, rtcR, zraP | Phage shock protein, Zn-resistence system, Acetoacetate metabolism |
33 | dsdC, dsdXA, ebgAC, ebgR, fucAO, fucPIKUR, lacI, lacZYA, malI, malXY, melAB, melR, uhpA, uhpT, yiaJ, yiaKLMNOPQRS | Lactose, maltose, fucose, dehydroascorbate, xylulose, melibiose transport and metabolism |
34 | aroF_tyrA, aroG, aroH, aroL_yaiA_aroM, aroP, mtr, trpLEDCBA, trpR, tyrP, tyrR | Aromatic amino acid synthesis |
35 | bioA, bioBFCD, birA_murA | Biotin synthesis |
36 | cbl, cysB, cysDNC, cysJIH, cysK, cysPUWAM, ssuEADCB, tauABCD | Sulfur metabolism, cysteine synthesis, Taurine utilization |
37 | exuR, exuT, uidR, uidABC, uxaCA, uxuABR | Utilization of hexUronide |
38 | lexA_dinF, polB, recA, recN, rpsU_dnaG_rpoD, ssb, sulA, umuDC, uvrA, uvrB, uvrC, uvrD | DNA recombination and repair, UV resistent |
39 | phnCDE_f73_phnFGHIJKLMNOP, phoA, phoBR, phoE, pstSCAB_phoU | Phosphate metabolism |