Table 1.

The genes included in the E. coli metabolic genotype (21)

Central metabolism (EMP, PPP, TCA cycle, electron transport)	aceA, aceB, aceE, aceF, ackA, acnA, acnB, acs, adhE, agp, appB, appC, atpA, atpB, atpC, atpD, atpE, atpF, atpG, atpH, atpI, cydA, cydB, cydC, cydD, cyoA, cyoB, cyoC, cyoD, dld, eno, fba, fbp, fdhF, fdnG, fdnH, fdnI, fdoG, fdoH, fdoI, frdA, frdB, frdC, frdD, fumA, fumB, fumC, galM, gapA, gapC_1, gapC_2, glcB, glgA, glgC, glgP, glk, glpA, glpB, glpC, glpD, gltA, gnd, gpmA, gpmB, hyaA, hyaB, hyaC, hybA, hybC, hycB, hycE, hycF, hycG, icdA, lctD, ldhA, lpdA, malP, mdh, ndh, nuoA, nuoB, nuoE, nuoF, nuoG, nuoH, nuoI, nuoJ, nuoK, nuoL, nuoM, nuoN, pckA, pfkA, pfkB, pflA, pflB, pflC, pflD, pgi, pgk, pntA, pntB, ppc, ppsA, pta, purT, pykA, pykF, rpe, rpiA, rpiB, sdhA, sdhB, sdhC, sdhD, sfcA, sucA, sucB, sucC, sucD, talB, tktA, tktB, tpiA, trxB, zwf, pgl (30), maeB (30)
Alternative carbon source	adhC, adhE, agaY, agaZ, aldA, aldB, aldH, araA, araB, araD, bglX, cpsG, deoB, fruK, fucA, fucI, fucK, fucO, galE, galK, galT, galU, gatD, gatY, glk, glpK, gntK, gntV, gpsA, lacZ, manA, melA, mtlD, nagA, nagB, nanA, pfkB, pgi, pgm, rbsK, rhaA, rhaB, rhaD, srlD, treC, xylA, xylB
Amino acid metabolism	adi, aldH, alr, ansA, ansB, argA, argB, argC, argD, argE, argF, argG, argH, argI, aroA, aroB, aroC, aroD, aroE, aroF, aroG, aroH, aroK, aroL, asd, asnA, asnB, aspA, aspC, avtA, cadA, carA, carB, cysC, cysD, cysE, cysH, cysI, cysJ, cysK, cysM, cysN, dadA, dadX, dapA, dapB, dapD, dapE, dapF, dsdA, gabD, gabT, gadA, gadB, gdhA, glk, glnA, gltB, gltD, glyA, goaG, hisA, hisB, hisC, hisD, hisF, hisG, hisH, hisI, ilvA, ilvB, ilvC, ilvD, ilvE, ilvG_1, ilvG_2, ilvH, ilvI, ilvM, ilvN, kbl, ldcC, leuA, leuB, leuC, leuD, lysA, lysC, metA, metB, metC, metE, metH, metK, metL, pheA, proA, proB, proC, prsA, putA, sdaA, sdaB, serA, serB, serC, speA, speB, speC, speD, speE, speF, tdcB, tdh, thrA, thrB, thrC, tnaA, trpA, trpB, trpC, trpD, trpE, tynA, tyrA, tyrB, ygjG, ygjH, alaB (42), dapC (43), pat (44), prr (44), sad (45), methylthioadenosine nucleosidase (46), 5-methylthioribose kinase (46), 5-methylthioribose-l-phosphate isomerase (46), adenosyl homocysteinase (47), l-cysteine desulfhydrase (44), glutaminase A (44), glutaminase B (44)
Purine & pyrimidine metabolism	add, adk, amn, apt, cdd, cmk, codA, dcd, deoA, deoD, dgt, dut, gmk, gpt, gsk, guaA, guaB, guaC, hpt, mutT, ndk, nrdA, nrdB, nrdD, nrdE, nrdF, purA, purB, purC, purD, purE, purF, purH, purK, purL, purM, purN, purT, pyrB, pyrC, pyrD, pyrE, pyrF, pyrG, pyrH, pyrI, tdk, thyA, tmk, udk, udp, upp, ushA, xapA, yicP, CMP glycosylase (48)
Vitamin & cofactor metabolism	acpS, bioA, bioB, bioD, bioF, coaA, cyoE, cysG, entA, entB, entC, entD, entE, entF, epd, folA, folC, folD, folE, folK, folP, gcvH, gcvP, gcvT, gltX, glyA, gor, gshA, gshB, hemA, hemB, hemC, hemD, hemE, hemF, hemH, hemK, hemL, hemM, hemX, hemY, ilvC, lig, lpdA, menA, menB, menC, menD, menE, menF, menG, metF, mutT, nadA, nadB, nadC, nadE, ntpA, pabA, pabB, pabC, panB, panC, panD, pdxA, pdxB, pdxH, pdxJ, pdxK, pncB, purU, ribA, ribB, ribD, ribE, ribH, serC, thiC, thiE, thiF, thiG, thiH, thrC, ubiA, ubiB, ubiC, ubiG, ubiH, ubiX, yaaC, ygiG, nadD (49), nadF (49), nadG (49), panE (50), pncA (49), pncC (49), thiB (51), thiD (51), thiK (51), thiL (51), thiM (51), thiN (51), ubiE (52), ubiF (52), arabinose-5-phosphate isomerase (22), phosphopantothenate-cysteine ligase (50), phosphopantothenate-cysteine decarboxylase (50), phospho-pantetheine adenylyltransferase (50), dephosphoCoA kinase (50), NMN glycohydrolase (49)
Lipid metabolism	accA, accB, accD, atoB, cdh, cdsA, cls, dgkA, fabD, fabH, fadB, gpsA, ispA, ispB, pgpB, pgsA, psd, pssA, pgpA (53)
Cell wall metabolism	ddlA, ddlB, galF, galU, glmS, glmU, htrB, kdsA, kdsB, kdtA, lpxA, lpxB, lpxC, lpxD, mraY, msbB, murA, murB, murC, murD, murE, murF, murG, murI, rfaC, rfaD, rfaF, rfaG, rfaI, rfaJ, rfaL, ushA, glmM (54), lpcA (55), rfaE (55), tetraacyldisaccharide 4′ kinase (55), 3-deoxy-d-manno-octulosonic-acid 8-phosphate phosphatase (55)
Transport processes	araE, araF, araG, araH, argT, aroP, artI, artJ, artM, artP, artQ, brnQ, cadB, chaA, chaB, chaC, cmtA, cmtB, codB, crr, cycA, cysA, cysP, cysT, cysU, cysW, cysZ, dctA, dcuA, dcuB, dppA, dppB, dppC, dppD, dppF, fadL, focA, fruA, fruB, fucP, gabP, galP, gatA, gatB, gatC, glnH, glnP, glnQ, glpF, glpT, gltJ, gltK, gltL, gltP, gltS, gntT, gpt, hisJ, hisM, hisP, hisQ, hpt, kdpA, kdpB, kdpC, kgtP, lacY, lamB, livF, livG, livH, livJ, livK, livM, lldP, lysP, malE, malF, malG, malK, malX, manX, manY, manZ, melB, mglA, mglB, mglC, mtlA, mtr, nagE, nanT, nhaA, nhaB, nupC, nupG, oppA, oppB, oppC, oppD, oppF, panF, pheP, pitA, pitB, pnuC, potA, potB, potC, potD, potE, potF, potG, potH, potI, proP, proV, proW, proX, pstA, pstB, pstC, pstS, ptsA, ptsG, ptsI, ptsN, ptsP, purB, putP, rbsA, rbsB, rbsC, rbsD, rhaT, sapA, sapB, sapD, sbp, sdaC, srlA_1, srlA_2, srlB, tdcC, tnaB, treA, treB, trkA, trkG, trkH, tsx, tyrP, ugpA, ugpB, ugpC, ugpE, uraA, xapB, xylE, xylF, xylG, xylH, fruF (56), gntS (57), metD (43), pnuE (49), scr (56)

The in silico E. coli MG1655 metabolic genotype used herein is available on the web: http://gcrg.ucsd.edu/downloads.html.