Table S1: Stoichiometric Equations Used for Metabolic Flux Analysis in Tkt Deficient Bacillus

Table S1: Stoichiometric equations used for metabolic flux analysis in tkt deficient Bacillus pumilus ATCC 21951

Sr no / Reaction / Enzyme / EC number
Glycolysis pathway
R1 / Glc + ATP  G6P + ADP / Glucokinase / 2.7.1.2
R2 / G6P  F6P / Phosphoglucose isomerase / 5.3.1.9
R3 / F6P + ATP F16dP + ADP / Phosphofructokinase / 2.7.1.11
R4 / F16DP G3P + DHAP / Fructose-1,6-bisphosphatate aldolase / 4.1.2.13
R5 / DHAP  G3P / Triosphosphate Isomerase / 5.3.1.1
R6 / G3P + Pi + NAD+G13Bp + NADH / Glyceraldehyde-3-phosphate dehydrogenase-A complex / 1.2.1.12
R7 / G13bP + ADP 3-PG + ATP / Phosphoglycerate kinase / 2.7.2.3
R8 / 3-PG  PEP / Phosphoglycerate mutase 1
Enolase / 5.4.2.1
4.2.1.11
R9 / PEP + ADP  PYR + ATP / Pyruvate kinase / 2.7.1.40
R10 / PYR + COA + NAD+ NADH + CO2 + AcCoA / Pyruvate dehydrogenase / 1.2.4.1
Pentose phosphate pathway
R11 / G6P + NADP+ D6PGL + NADPH / Glucose 6-phosphate-1-dehydrogenase / 1.1.1.49
R12 / D6PGL  D6PGC / 6-Phosphogluconolactonase / 3.1.1.31
R13 / D6PGC + NADP+ NADPH + CO2 + RL5P / 6-Phosphogluconate dehydrogenase (decarboxylating) / 1.1.1.44
R14 / RL5P  X5P / Ribulose phosphate 3-epimerase / 5.1.3.1
R15 / RL5P  R5P / Ribose-5-phosphate isomerase A / 5.3.1.6
R16 / R5P D-ribose / Ribokinase / 2.7.1.15
TCA cycle
R17 / AcCoA + OA  CoA + CIT / Citrate synthase / 4.1.3.7
R18 / CIT  ICIT / Aconitase A / 4.2.1.3
R19 / ICIT + NAD+ CO2 + NADH + AKG / Isocitrate dehydrogenase / 1.1.1.42
R20 / AKG + NAD+ + COA  CO2 + NADH + SUCCoA / 2-Ketoglutarate dehydrogenase / 1.2.4.2
R21 / SUCCoA + ADP + Pi ATP + CoA + SUCC / Succinyl-CoA synthetase / 6.2.1.5
R22 / SUCC + FAD+ FADH2 + FUM / Succinate dehydrogenase / 1.3.99.1
R23 / FUM  MAL / Fumarase A / 4.2.1.2
R24 / MAL + NAD+ NADH + OA / Malate dehydrogenase / 1.1.1.37
Analplerosis reaction
R25 / PYR + ATP + CO2 OA + ADP + Pi / pyruvate carboxylase / 6.4.1.1
Gluconeogenesis
R26 / OA + ATP  PEP + CO2 + ADP + Pi / Phosphoenolpyruvate carboxykinase / 4.1.1.49
Malic enzyme
R27 / MAL + NAD+ PYR + CO2 + NADH + H+ / Malic enzyme (NAD) / 1.1.1.38
R28 / MAL + NADP+ PYR +CO2 + NADPH + H+ / Malic enzyme (NADP) / 1.1.1.40
Branches from Glycolysis
R29 / 2 PYR  ALC + CO2 / Acetolactate synthase / 2.2.1.6
R30 / ALC  Acetoin + CO2 / Acetolactat-Decarboxylase / 4.1.1.5
R31 / AcCoA + AMP + PPi  Acetate + ATP + CoA / Phosphotransacetylase,
Acetate kinase A / 2.3.1.8
2.7.2.1
R32 / Acetate + ATP + CoA  AcCoA + AMP + PPi / Acetyl-CoA synthetase / 6.2.1.1
R33 / Acetoin + NADH 2-3Butanediol + NAD+ / D-butanediol dehydrogenase,
Acetoin Dehydrogenase / 1.1.1.4
1.1.15
R34 / PYR + NADH + H+ Lactate + NAD / D-Lactate dehydrogenase 1 / 1.1.1.28
Electron transport chain/oxidative phosphorilazation
R35 / 0.5 O2 + NADH + P/O ADP  P/O ATP + NAD+ / ATP synthase / 3.6.3.14
R36 / 0.5 O2 + FADH2 + P/O ADP  P/O ATP + NAD+ / ATP synthase / 3.6.3.14
Transhydrogenase reactions
R37 / NADPH +NAD+ NADP+ + NADH / Pyridine nucleotide transhydrogenase / 1.6.1.1
R38 / NADH + NADP+ + 0.25 ATP  NADPH + NAD+ / Pyridine nucleotide transhydrogenase / 1.6.1.1
Biosynthesis of serine family amino acids
R39 / 3-PG + Glu Ser + AKG + NADH + Pi / Phosphoglycerate dehydrogenase,
Phosphoserine transaminase,
Phosphoserine phosphatase / 1.1.1.95
2.6.1.52
3.1.3.3
R40 / Ser + THF  Gly + MetTHF / Glycine hydroxymethyltransferase / 2.1.2.1
R41 / Ser + AcCoA + H2S Cys + Acetate / Serine transacetylase,
O-acetylserine sulfhydrylase / 2.3.1.30
2.5.1.47
Biosynthesis of alanine family amino acids
R42 / 2 Pyr + NADPH  Kval / Pyruvate dehydrogenase (acetyl-transferring),
Acetolactate synthase,
Ketol-acid reductoisomerase,
Dihydroxy-acid dehydratase / 1.2.4.1
2.2.1.6
1.1.1.86
4.2.1.9
R43 / Kval + Glu  Val + AKG / Transaminase B / 2.6.1.42
R44 / Kval + AcCoA + Glu  Leu + AKG + NADH + CO2 / 2-isopropylmalate synthase,
Isopropylmalate isomerase,
3-isopropylmalate dehydrogenase,
Leucine dehydrogenase / 2.3.3.13
4.2.1.33
1.1.1.85
1.4.1.9
R45 / Pyr + Glu  Ala + AKG / Alanine transaminase / 2.6.1.2
R46 / RL5P + ATP PRPP + AMP / Ribose-5-phosphate isomerase B,
Ribose-phosphate pyrophosphokinase / 5.3.1.6
2.7.6.1
R47 / PRPP + ATP + Gln  His + PRAIC +AKG + 2 PPi + 2 NADH + Pi / ATP phosphoribosyltransferase,
Phosphoribosyl-ATP pyrophosphohydrolase,
Phosphoribosyl-AMP cyclohydrolase,
Phosphoribosylformimino-5-aminoimidazole carboxamideribotide isomerase,
Imidazoleglycerol-phosphate dehydratase,
Histidinol-phosphate aminotransferase
Histidinol-phosphatase
Histidinol dehydrogenase / 2.4.2.17
3.6.1.31
3.5.4.19
5.3.1.16
4.2.1.19
2.6.1.9
3.1.3.15
1.1.1.23
Biosynthesis of aspartic acid family amino acids
R48 / OA + Glu  Asp + AKG / L-aspartate oxidase / 1.4.3.16
R49 / Asp + Gln + ATP  Asn + Glu + AMP + PPi / Asparagine synthase / 6.3.5.4
R50 / Asp + ATP + NADPH  AspSa + ADP + Pi / Aspartate kinase,
Aspartate-semialdehyde dehydrogenase / 2.7.2.4
1.2.1.11
R51 / AspSa + Pyr + NADPH  Tet / Dihydrodipicolinate synthase,
Dihydrodipicolinate reductase / 4.2.1.52
1.3.2.6
R52 / Tet + AcCoA + Glu  AKG + acetate + mDAP / Tetrahydropicolinate succinylase,
N-succinyldiaminopimelate aminotransferase,
Succinyl-diaminopimelate desuccinylase,
Diaminopimelate epimerase / 2.3.1.117
2.6.1.17
3.5.1.18
5.1.1.7
R53 / mDAP Lys + CO2 / Diaminopimelate decarboxylase / 4.1.1.20
R54 / AspSA + NADPH Hser / Homoserine dehydrogenase / 1.1.1.3
R55 / HSer+ATP Thr + ADP + Pi / Homoserine kinase,
Threonine synthase / 2.7.1.39
4.2.3.1
R56 / Thr + Pyr + NADPH + Glu  Ile + AKG + NH3 + CO2 / Threonine dehydratase,
Acetolactate synthase,
Ketol-acid reductoisomerase,
Dihydroxy-acid dehydratase,
Transaminase B / 4.3.1.19
2.2.1.6
1.1.1.86
4.2.1.9
2.6.1.42
R57 / AcCoA + Cys + HSer + H2S + MTHF  Met + Pyr + 2 acetate + NH3 + THF / Homoserine O-succinyltransferase,
Cystathionine gamma-synthase,
Cystathionine γ-lyase,
Cystathionine beta-lyase,
O-acetyl-L-homoserine sulfhydrolase,
Methionine synthase,
Homocysteine methylase / 2.3.1.46
2.5.1.48
4.4.1.1
4.4.1.8
2.5.1.49
2.1.1.13
2.1.1.14
Biosynthesis of glutamic acid family amino acids
R58 / AKG + NH3 + NADPH Glu / Glutamate synthase (NADPH) / 1.4.1.13
R59 / Glu + ATP + NH3  Gln + ADP + Pi / Glutamine synthetase / 6.3.1.2
R60 / Glu + ATP + 2 NADPH Pro + ADP + Pi / 1-pyrroline dehydrogenase,
Pyrroline-5-carboxylate reductase / 1.5.1.12
1.5.1.2
R61 / 2Glu + AcCoA + ATP + NADPH Orn+AKG+ADP+Pi / 1-pyrroline dehydrogenase,
Ornithine aminotransferase / 1.5.1.12
2.6.1.13
R62 / Orn + CaP Citr+Pi / Ornithine carbamoyltransferase / 2.1.1.33
R63 / Citr + Asp + ATP Arg + Fum + AMP + PPi / Argininosuccinate synthase
Argininosuccinate lyase / 6.3.4.5
4.3.2.1
Biosynthesis of nucleotides:
Purine synthesis
R64 / PRPP + 2 Gln + Asp + 2 H2O + CO2 + Gly + 4 ATP + F10THF  2 Glu + PPi+ 4 ADP + 4 Pi + THF + PRAIC + FUM / Amidophosphoribosyltransferase
Phosphoribosylglycinamide synthetase
Phosphoribosylglycinamide formyltransferase
Phosphoribosylformylglycinamidine synthase
Phosphoribosylaminoimidazole synthetase
Phosphoribosylaminoimidazole carboxylase / 2.4.2.14
6.3.4.13
2.1.2.2
6.3.5.3
6.3.3.1
4.1.1.21
R65 / PRAIC + F10THF  IMP + THF / phosphoribosylaminoimidazolesuccinocarboxamide synthase
Adenylosuccinate lyase
Phosphoribosylaminoimidazolecarboxamide
formyltransferase
IMP cyclohydrolase / 6.3.2.6
4.3.2.2
2.1.2.3
3.5.4.10
R66 / IMP + Gln + ATP NADH + GMP + Glu + AMP + PPi / Inositol-5-monophosphate dehydrogenase
Guanosine 5'-monophosphate synthetase / 1.1.1.205
6.3.5.2
R67 / GMP + ATP GDP + ADP / Guanylate kinase / 2.7.4.8
R68 / ATP + GDP ADP + GTP / Nucleoside diphosphate kinase
Pyruvate kinase / 2.7.4.6
2.7.1.40
R69 / ADP + GTP ATP + GDP / Nucleoside diphosphate kinase
Pyruvate kinase / 2.7.4.6
2.7.1.40
R70 / NADPH + ATP dATP / Nucleoside diphosphate kinase
Pyruvate kinase
Ribonucleoside-diphosphate reductase / 2.7.4.6
2.7.1.40
1.17.4.1
R71 / NADPH + GDP + ATP  ADP + dGTP / Nucleoside diphosphate kinase
Ribonucleotide-diphosphate reductase subunit alpha
Ribonucleoside-diphosphate reductase / 2.7.4.6
1.17.4.1
2.7.1.40
R72 / IMP + GTP +Asp  GDP + Pi + FUM +AMP / Adenylosuccinate synthetase
Adenylosuccinate lyase / 6.3.4.4
4.3.2.2
R73 / AMP + ATP 2 ADP / Adenylate kinase / 2.7.4.3
Pyrimidine synthesis
R74 / PRPP + Asp + CaP  UMP + NADH + PPi+ CO2 / Aspartate carbamoyltransferase
Dihydroorotase
Dihydroorotate oxidase
Orotate phosphoribosyltransferase
Orotidine-5'-phosphate decarboxylase / 2.1.3.2
3.5.2.3
1.3.3.1
2.4.2.10
4.1.1.23
R75 / UMP + ATP  UDP + ADP / Cytidylate kinase
UMP kinase / 2.7.4.14
2.7.4.22
R76 / UDP + ATP  ADP + UTP / Nucleoside diphosphate kinase / 2.7.4.6
R77 / UTP + NH3 +ATP CTP+ ADP + Pi / CTP synthetase / 6.3.4.2
R78 / ATP + NADPH + CDP  dCTP + ADP / Ribonucleoside-diphosphate reductase
Nucleoside diphosphate kinase / 1.17.4.1
2.7.4.6
R79 / CDP + ATP  CTP + ADP / Nucleoside diphosphate kinase / 2.7.4.6
R80 / CTP + ADP CDP + ATP / Nucleoside diphosphate kinase / 2.7.4.6
R81 / UDP + MetTHF + 2 ADP + NADPH dTTP + DHF + 2 ADP +PPi / Ribonucleoside-diphosphate reductase
Thymidylate kinase
Thymidylate synthase
Nucleoside diphosphate kinase / 1.17.4.1
2.7.4.9
2.1.1.45
2.7.4.6
Biosynthesis of one carbon unit
R82 / DHF + NADPH THF + NADP+ / Dihydrofolate reductase / 1.5.1.3
R83 / MetTHF + CO2 + NH3 + NADH Gly + THF / Glycine hydroxymethyltransferase
Aminomethyltransferase / 2.1.2.1
2.1.2.10
R84 / MetTHF + NADPH MTHF / Methylenetetrahydrofolate reductase (ferredoxin) / 1.5.7.1
R85 / MetTHF MeTHF + NADPH / N5,N10-methylenetetrahydrofolate dehydrogenase / 1.5.1.5
R86 / MeTHF F10THF / Methenyltetrahydrofolate cyclohydrolas / 3.5.4.9
R87 / Gly + THF MetTHF + NH3 + NADH + CO2 / Glycine hydroxymethyltransferase
Aminomethyltransferase / 2.1.2.1
2.1.2.10
Biosynthesis of fatty acid
R88 / G3P + NADPH GL3P / Glycerol 3-phosphate dehydrogenase (NADP+)
Glycerol-3-phosphate dehydrogenase / 1.1.1.94
1.1.95.5
R89 / 7 AcCoA + 6 ATP + 12 NADPH  C14:0 + 6 ADP + 6 Pi / Acetyl-CoA carboxylase;
[Acyl-carrier-protein] S-malonyltransferase
3-oxoacyl-(acyl carrier protein) synthase II
3-oxoacyl-[acyl-carrier-protein]reductase (NADH)
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Enoyl-(acyl carrier protein) reductase
Acyl-[acyl-carrier-protein] hydrolase / 6.4.1.2
2.3.1.39
2.3.1.41
1.1.1.212
4.2.1.60
1.3.1.9
3.1.2.14
R90 / 7 AcCoA + 6 ATP + 11 NADPH  C14:1 + 6 ADP + 6 Pi / All enzyme for C14:0,
Delta-9 desaturase / 1.4.99.5
R91 / 8.2 AcCoA + 7.2 ATP + 14 NADPH  FA+ 7.2 ADP + 7.2 Pi / Acetyl-CoA acetyltransferase
Enoyl-CoA hydratase
Acyl-CoA synthetase / 2.3.1.9
4.2.1.17
6.2.1.3
R92 / 2 ATP + CO2 + Gln  CaP + Glu + 2 ADP + Pi / Carbamoyl phosphate synthetase II / 6.3.5.5
Other biomass components
R93 / F6P + Gln + AcCoA + UTP  UDPNAG + Glu + PPi / Glutamine-fructose-6-phosphate transaminase
Phosglucosaminemut reaction
Glucosamine-phosphate N-acetyltransferase
UDP-N-acetylglucosamine diphosphorylase / 2.6.1.16
Not assign
2.3.1.4
2.7.7.23
R94 / PEP + NADPH + UDPNAG UDPNAM + Pi / EP-UDP-GlcNAc synthase (Mur A)
EP-UDP-GlcNAc reductase (Mur B) / -
-
R95 / RL5P + PEP + CTP CMPKDO + PPi + 2 Pi / D-arabinose-5-phosphate isomerase
3-Deoxy-D-manno-octulosonate (KDO)-8-phosphate synthetase
CMP-KDO synthase / 5.3.1.13
2.5.1.55
2.7.7.38
R96 / Ser + CTP + ATP CDPEtN + ADP + PPi + CO2 / CDP-diacylglycerol—serine O-phosphatidyltransferase
Phosphatidylserine decarboxylase
Phospholipase C
Phosphorylethanolamine transferase / 2.7.8.8
4.1.1.65
3.1.4.3
2.7.7.14
R97 / G6P G1P / Phosphoglucomutase / 5.4.2.2
R98 / UTP + G1P  UDPGlc + PPi / UTP-glucose-1-phosphate uridylyltransferase / 2.7.7.9
ATP maintainence
R99 / ATP  ADP (for maintenance)
Transport of extracellular metabolites
R100 / Alaex + Hext Ala
R101 / Argex + Hext Arg
R102 / Asnex + Hext Asn
R103 / Aspex + Hext Asp
R104 / Cysex + Hext Cys
R105 / Hisex + Hext His
R106 / Glnex + Hext Gln
R107 / Gluex + Hext Glu
R108 / Glyex + Hext Gly
R109 / Ileex + Hext Ile
R110 / Leuex + Hext Leu
R111 / Lysex + Hext Lys
R112 / Metex + Hext Met
R113 / Ornex + Hext Orn
R114 / Pheex + Hext Phe
R115 / Proex + Hext Pro
R116 / Serex+ Hext Ser
R117 / Trpex + Hext Trp
R118 / Tyrex + Hext Tyr
R119 / Threx+ Hext  Thr
R120 / Valex + Hext Val
R121 / 2ATP + 4 NADPH AMP + ADP + H2S + Ppi + Pi
R122 / CO2 CO2ex / Carbon dioxide transport / Diffusion
R123 / O2exO2 / Oxygen transport / Diffusion
R124 / D-ribose D-riboseex
R125 / Acetate + H+Acetateex
R126 / Acetoin Acetoinex
R127 / 2-3Butanediol 2-3Butanediol ex
R128 / Lactate + H+Lactateex
R129 / Glcex + HextGlc / Glucose transporter / Proton symport
R130 / NH3exNH3
Biomass growth
R131 / 0.594 Ala + 0.198 Arg + 0.143 Asn + 0.284 Asp + 0.060 Cys + 0.272 Gln + 0.367 Glu + 0.495 Gly + 0.086 His + 0.288 Ile + 0.368 Leu + 0.342 Lys + 0.118 Met + 0.059 Orn + 0.175 Pro + 0.304 Ser + 0.239 Thr + 0.335 Val + 0.136 UTP + 0.126 CTP + 0.203 GTP + 0.0246 dATP + 0.0254 dGTP + 0.0254 dCTP + 0.0246 dTTP + 0.083 GL3P + 0.0238 C14:0 + 0.0238 C14:1 + 0.15 FA + 0.095 UDPNAG + 0.095 UDPNAM + 0.111 UDPGlc + 0.154 + G1P+ 0.0235 CMPKDO + 0.0235 CDPEtN + 22.738 ATP  1g Biomass + 22.378 ADP + 22.738 Pi
R132 / BiomassBiomassex
Abbreviation
3-PG / 3-phospho glycerate
AcCoA / Acetyl coenzyme A
Ala / Alanine
ALC / Acetolactate
AKG / Α-ketoglutarate
Arg / Arginine
Asn / Asparagine
ADP / Adenosine 5’-diphosphate
AMP / Adenosine 5’-monophosphate
Asp / Aspartate
AspSa / Aspartate semialdehyde
ATP / Adenosine 5’-triphosphate
C14:0 / Myristic acid
C14:1 / Hydroxymyristic acid
CaP / Carbamoyl phosphate
CDP / Cytidine 5’ diphosphate
CDPEtN / CDP-ethanolamine
CIT / Citrate
Citr / Citruline
CMPKDO / CMP-3-deoxy-D-manno-octulosonic acid
CO2 / Carbon dioxide
CoA / Coenzyme A
CTP / Cytidine-5′-triphosphate
Cys / L-cysteine
D6PGC / D-6-Phosphate-glucono-delta-lactone
D6PGL / D-6-Phosphate-gluconate
dATP / 2′-deoxy-ATP
dCTP / 2′-deoxy-CTP
DHF / 7,8-dihydrofolate
DHAP / Dihydroxyacetone phosphate
dGTP / 2′-deoxy-GTP
dTTP / 2′-deoxy-TTP
F16dP / Fructose-1-6-diphosphate
F6P / Fructose-6-phosphate
F10THF / N10-formyl-THF
FA / Fatty acids
FADH2 / Flavine adeninedinucleotide
FUM / Fumarate
G1P / Glucose-1-phosphate
G13bP / 1,3-bis-Phosphoglycerate
G3P / Glycerate-3-phosphate
G6P / Glucose-6-phosphate
GDP / Guanosine-5′-diphosphate
GL3P / Glycerol-5’-phosphate
Glc / Glucose
Gln / L-glutamine
Glu / L-glutamate
Gly / L- glycine
GMP / Guanosine-5′-monophosphate
GTP / Guanosine-5′-triphosphate
His / L- histidine
Hser / Homoserine
ICIT / Isocitrate
Ile / L-Isoleucine
IMP / Inosinemonophosphate
Kval / Ketovaline
Leu / L-leucine
Lys / L-lysine
MAL / Malate
mDAP / Meso-diaminopimelate
Met / L-methionine
MeTHF / N5,N10-methenyl-THF
MetTHF / N5,N10-methylene-THF
MTHF / N5-methyl-THF
NADH / Nicotinamide-adeninedinucleotide (reduced)
NADPH / Nicotinamide-adeninedinucleotide phosphate (reduced)
NH3 / Ammonia
O2 / Oxygen
OA / Oxaloacetate
Orn / Ornithine
Pi / Phosphate
PDH / Pyruvate dehydrogenase
PEP / Phosphoenolpyruvate
Phe / L-phenylalanine
PYR / Pyruvate
PRAIC / 5′-phosphoribosyl-4-carboxamide-5-aminoimidazole
Pro / L-proline
PRPP / 5-phospho-D-ribosylpyrophosphate
R5P / Ribose-5-phosphate
RL5P / Ribulose-5-phosphate
Ser / L-serine
SUCC / Succinate
SUCCoA / Succinate coenzyme A
Tet / L-2,3,4,5-tetrahydrodipicolinate
THF / Tetrahydrofolate
Thr / L-threonine
Tyr / L-tyrosine
UDP / Uridine-5′-diphosphate
UDPGlc / UDP-glucose
UDPNAG / UDP-N-acetyl-glucosamine
UDPNAM / UDP-N-acetyl-muramic acid
UMP / Uridine-5′-monophosphate
UTP / Uridine-5′-triphosphate
Val / L-valine
X5P / Xylulose-5-phosphate