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Table 2 Comparison of metabolic reaction fluxes of amino acids biosynthetic reactions between minimal and complex media

From: Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27

Reaction ID

Enzyme name (Gene)

Reaction details

Complex media

Minimal media

   

(LB < L < UB)

(LB < L < UB)

R192

Alanine dehydrogenase ( ald )

H[c] + NADH[c] + PYR[c] + NH4[c] < = > L_ALA[c] + NAD[c] + H2O[c]

-0.031 < -0.031 < -0.031

0.234 < 0.234 < 2.416

R521

Asparagine synthase (asnB)

L_ASP[c] + L_GLN[c] + ATP[c] + H2O[c] < = > L_GLU[c] + L_ASN[c] + PPi[c] + H[c] + AMP[c]

-1.808 < -1.808 < -1.783

-0.537 < -0.537 < -0.522

R198

Aspartate aminotransferase (aspC)

L_ASP[c] + AKG[c] < = > L_GLU[c] + OAC[c]

-1.782 < -1.782 < -1.782

-0.416 < -0.416 < -0.416

R205

Glutamine synthetase (gln)

L_GLU[c] + ATP[c] + NH4[c] - > L_GLN[c] + ADP[c] + Pi[c] + H[c]

-1.793 < -1.793 < -1.793

-0.474 < -0.474 < -0.474

R202

Glutamate dehydrogenase (gdh)

L_GLU[c] + NADP[c] + H2O[c] < = > H[c] + NADPH[c] + AKG[c] + NH4[c]

-9.830 < -9.145 < 4.713

-9.288 < -8.813 < 2.977

R227

Cysteine synthase ( cysM )

OAC_SER[c] + H2S[c] - > L_CYS[c] + H[c] + AC[c]

0 < 0 < 0

0 < 0.005 < 0.005

R235

Methionine synthase ( metH )

L_HCYS[c] + 5MTHF[c] - > L_MET[c] + H[c] + THF[c]

0 < 0 < 0

0 < 0.009 < 0.009

R272

N2-acetyl-L-lysine deacetylase (lysK)

H2O[c] + N2AC_L_LYS[c] - > L_LYS[c] + AC[c]

0.229 < 0.229 < 0.229

0.05 < 0.05 < 0.05

R651

3-phosphoserine phosphatase (serB)

H2O[c] + PPTD_SER[c] - > L_SER[c] + Pi[c]

0 < 0 < 0

0 < 1.072 < 2.545

R655

Serine hydroxymethyltransferase (glyA)

L_SER[c] + THF[c] - > L_GLY[c] + H2O[c] + METHF[c]

0 < 0 < 0

0 < 0.512 < 6.42

R213

Serine hydroxymethyltransferase (glyA)

L_GLY[c] + H2O[c] + 5_10_MNTHF[c] < = > L_SER[c] + THF[c]

0.135 < 0.135 < 0.135

-1.787 < -0.442 < 3.993

R212

Tryptophan synthase (trpA)

L_SER[c] + IND_GLYP[c] < = > L_TRP[c] + H2O[c] + GAP[c]

0.054 < 0.054 < 0.054

0.026 < 0.026 < 0.026

R221

Threonine synthase (thrC)

H2O[c] + OP_HSER[c] - > L_THR[c] + Pi[c]

0.0714 < 0.0714 < 0.0714

0.063 < 0.063 < 0.063

R245

Branched-chain amino acid aminotransferase ( ilvE )

L_VAL[c] + AKG[c] < = > L_GLU[c] + 2K3M_BUT[c]

0.113 < 0.113 < 0.113

-0.068 < -0.068 < -0.068

R244

Branched-chain amino acid aminotransferase ( ilvE )

L_GLU[c] + 4M_2OPENTN[c] < = > L_LEU[c] + AKG[c]

-1.179 < -1.179 < -1.179

0.154 < 0.154 < 0.154

R246

Branched-chain amino acid aminotransferase ( ilvE )

L_ILE[c] + AKG[c] < = > L_GLU[c] + 3M_2OPENTN[c]

0.478 < 0.478 < 0.478

-0.024 < -0.024 < -0.024

R341

Pyrroline-5-carboxylate reductase (ProC)

L_PRO[c] + NADP[c] < = > 2 H[c] + NADPH[c] + PYRR5CARB[c]

-0.432 < -0.432 < -0.432

-0.119 < -0.119 < -0.119

R195

Argininosuccinate lyase (argH)

L_ARG_SUCC[c] - > L_ARG[c] + FUM[c]

1.144 < 1.144 < 1.144

0.132 < 0.132 < 0.132

R297

Aspartate aminotransferase ( aat )

L_PHE[c] + AKG[c] < = > L_GLU[c] + PPYR[c]

0 < 0 < 0

-0.054 < -0.054 < -0.054

R284

Histidinol dehydrogenase (hisD)

2 NAD[c] + H2O[c] + L_HISN[c] - > L_HIS[c] + 3 H[c] + 2 NADH[c]

0.025 < 0.025 < 0.025

0.015 < 0.015 < 0.015

  1. The reactions which are highlighted in bold possess less flux in complex media. FVA was conducted to re-assure the simulated fluxes and the results are provided with the attainable lower and upper bounds identified from this analysis.