Table 6 Suggested targets for increasing citric acid output based on results from the evolutionary algorithm (primarily ranked by frequency and then by citric %increase)

R1447

Citrate exporter

CIT-e ↔ CIT

Up-regulate

8

R442

Diphosphatase

PPI + H₂O → 2*PI + H

Down-regulate

8

R209

Glycerol 3-phosphate dehydrogenase (FAD dependent)

GL3P + FADm → T3P2 + FADH2m

Down-regulate

7

R634

Phosphoribosyl amino imidazolesuccinocarbozamide synthetase

ASP + ATP + CAIR ↔ 2*H + PI + ADP + SAICAR

Down-regulate

7

R80

Acetate kinase

ATP + AC ↔ ADP + ACTP

Down-regulate

7

R188

Thiamin monophosphate phosphohydrolase

THMP + H₂O → THM + PI

Down-regulate

7

R443

Diphosphatase

PPIm + H₂O → 2*PIm + Hm

Down-regulate

7

R1122

ATP:ethanolamine O-phosphotransferase

ATP + ETHLA → ADP + PEA + H

Down-regulate

7

R22

Pyruvate carboxylase

ATP + PYR + H₂O + CO₂ → ADP + PI + OA + 2*H

Up-regulate

6

R636

IMP cyclohydrolase

AICAR + FTHF ↔ THF + PRFICA

Down-regulate

6

R398

4-Carboxymuconolactone decarboxylase

4CMUCL + 2*H → OAEL + CO₂

Down-regulate

6

R20

Phosphopyruvate hydratase

2PG ↔ PEP + H₂O

Down-regulate

6

NR18

Acetyl-CoA:carnitine O-acetyltransferase

ACCOAm + CARm ↔ COAm + ALCARm

Down-regulate

6

R23

Pyruvate carboxylase

ATPm + PYRm + H₂Om + CO₂m → ADPm + PIm + OAm + 2*Hm

Up-regulate

6

NR20

Acetyl-CoA:carnitine O-acetyltransferase

ACCOA + CAR ↔ COA + ALCAR

Down-regulate

6

R29

Ribose-5-phosphate isomerase

R5P ↔ RL5P

Down-regulate

6

R765

Nicotinate phosphoribosyltransferase

NICA + PRPP → NAMN + PPI

Down-regulate

6

R240

Phosphoglucomutase

R5P ↔ R1P

Down-regulate

6

R685

Allantoicase

ATT + H₂O ↔ UGC + UREA

Down-regulate

6

R644

Nucleoside-diphosphate kinase

ATP + DADP ↔ ADP + DATP

Down-regulate

6

R764

Nicotinamidase

NICD + H₂O ↔ NICA + NH3

Down-regulate

5

R397

3-Carboxy-cis,cis-muconate cycloisomerase

3CMUCO ↔ 4CMUCL

Down-regulate

5

R415

UDP-N-acetylglucosamine pyrophosphorylase

UTP + NAGA1P ↔ PPI + UDPNAG

Down-regulate

5

R512

Phosphoserine transaminase

PHP + GLU → AKG + 3PSER

Down-regulate

5

R607

Proline dehydrogenase

NADm + PROm → 2*Hm + NADHm + P5Cm

Down-regulate

5

R684

Allantoinase

ATN + H₂O ↔ ATT

Down-regulate

5

R707

Nucleoside-diphosphate kinase

DUDP + ATP ↔ DUTP + ADP

Down-regulate

5

R74

Formate oxidase

FOR + O₂ + H → H₂O₂ + CO₂

Down-regulate

5

R637

IMP cyclohydrolase

PRFICA ↔ H₂O + IMP

Down-regulate

5

R699

Nucleoside-diphosphate kinase

CTP + ADP ↔ CDP + ATP

Down-regulate

5

R630

Phosphoribosylglycinamide formyltransferase

FTHF + GAR → H + THF + FGAR

Down-regulate

5

R719

Uracil phosphoribosyltransferase

URA + PRPP → UMP + PPI + H

Down-regulate

5

R730

Cytosine deaminase

CYTS + H₂O + H → URA + NH₃

Down-regulate

5

R306

Ketohexokinase

ATP + FRU → ADP + F1P + H

Down-regulate

4

R648

Nucleoside-diphosphate kinase

ATP + GDP ↔ ADP + GTP

Down-regulate

4

R605

Pyrroline-5-carboxylate reductase

2*H + NADPH + P5C ↔ PRO + NADP

Down-regulate

4

R244

Ribulokinase

ATP + RL → ADP + RL5P + H

Down-regulate

4

R139

5-Formyltetrahydrofolate deformylase

FTHF + H₂O → FOR + THF + H

Down-regulate

4

R511

Phosphoglycerate dehydrogenase

NAD + 3PG ↔ H + NADH + PHP

Down-regulate

4

R16

Triosephosphate isomerase

T3P2 ↔ T3P1

Down-regulate

4

R27

Phosphogluconate dehydrogenase

D6PGC + NADP → RL5P + CO₂ + NADPH

Up-regulate

4

R54

Malate synthase

ACCOAp + H2Op + GLXp → MALp + COAp + Hp

Up-regulate

4

R450

Cytochrome c oxidase

2*FEROm + 0.5*O₂m + 6*Hm → 2*FERIm + H₂Om + 4*Ho

Up-regulate

4

R658

Purine nucleoside hydrolase

ADN + H₂O → AD + RIB

Down-regulate

3

R257

D-arabinitol 2-dehydrogenase(NAD +)

AOL + NAD → RL + NADH + H

Down-regulate

3

R1215

D-Glyceraldehyde:NAD + oxidoreductase

G + NADH + 2*H ↔ GLYAL + NAD + H₂O

Down-regulate

3

R1233

3'—5' Bisphosphate nucleotidase

PAP + H₂O → AMP + PI

Down-regulate

3

R674

Purine nucleosidase

GSN + H₂O → GN + RIB

Down-regulate

3

R769

NAD synthetase

ATP + DMNAD + GLN + H₂O ↔ AMP + PPI + NAD + GLU + 2*H

Down-regulate

3

R266

Gluconokinase

GLCNT + ATP → D6PGC + ADP + H

Down-regulate

3

R413

N-acetylglucosamine-6-phosphate deacetylase

NAGA6P + H₂O → GA6P + AC

Down-regulate

3

R458

ADP/ATP translocase

ADP + PI + ATPm + H2Om → ADPm + PIm + ATP + H₂O

Up-regulate

3

R720

dUTP pyrophosphatase

DUTP + H₂O → PPI + DUMP + 2*H

Down-regulate

2

R675

Guanine aminohydrolase

GN + H₂O ↔ XAN + NH₃

Down-regulate

2

R1242

Urea carboxylase

UREA + ATP + H₂O + CO₂ ↔ ADP + PI + UREAC + 2*H

Down-regulate

2

R189

ATP:thiamine diphosphotransferase

ATP + THM → AMP + THDP + 2*H

Down-regulate

2

R1214

Glycerate 3-kinase

ATP + G → ADP + 3PG + H

Down-regulate

2

R86

Lactoylglutathione lyase

RGT + MTHGXL ↔ LGT

Down-regulate

2

R716

Uridine kinase

URI + GTP → UMP + GDP + H

Down-regulate

2

R588

Chorismate mutase

CHOR → PHEN

Down-regulate

2

R695

Nucleoside-diphosphate kinase

UDP + ATP ↔ UTP + ADP

Down-regulate

2

R446

Respiratory-chain NADH dehydrogenase

NADH + Qm + 5*Hm → NAD + QH2m + 4*Ho

Up-regulate

2

R479

Ornithine transaminase

ORN + AKG → GLUGSAL + GLU

Up-regulate

2

R514

Glycine hydroxymethyltransferase

THF + SER ↔ H₂O + GLY + METTHF

Up-regulate

2

R713

ADP-ribose pyrophosphatase

ADPR + H₂O → AMP + R5P + 2*H

Down-regulate

2

R451

ATP synthase

ADPm + PIm + 4.5454*Ho → ATPm + H₂Om + 4.5454*Hm

Up-regulate

2

R76

Pyruvate dehydrogenase

PYRm + NADm + COAm → ACCOAm + NADHm + CO₂m + Hm

Up-regulate

2

R105

Glutamate decarboxylase

GLUm + Hm → GABAm + CO₂m

Down-regulate

1

R515

Threonine aldolase

GLY + ACAL ↔ THR

Down-regulate

1

R370

Kynurenine formamidase

FKYN + H₂O → FOR + KYN + H

Down-regulate

1

R1243

Allophanate hydrolase

UREAC + H₂O → 2*NH₃ + 2*CO₂

Down-regulate

1

R200

Aldehyde dehydrogenase (NADP+)

ACALm + NADPm + H₂Om → ACm + NADPHm + 2*Hm

Down-regulate

1

R135

Methylenetetrahydrofolate dehydrogenase (NADP +)

METHFm + NADPHm ↔ METTHFm + NADPm

Up-regulate

1

R784

5'-Nucleotidase

NAMN + H₂O → NAR + PI

Up-regulate

1

R728

Cytidine deaminase

CYTD + H₂O → URI + NH₃

Down-regulate

1

R211

Glycerol 3-phosphate dehydrogenase (NAD+ dependent)

H + T3P2 + NADH → GL3P + NAD

Up-regulate

1

R337

Phenylacetaldehyde dehydrogenase

PHAL + NADP + H₂O ↔ PHAC + NADPH + 2*H

Down-regulate

1

R205

Glycerol dehydrogenase

H + GLYAL + NADPH → GL + NADP

Down-regulate

1

R53

Isocitrate lyase

ICITp → SUCCp + GLXp

Up-regulate

1

R445

Respiratory-chain NADH dehydrogenase

NADHm + Qm + 5*Hm → NADm + QH2m + 4*Ho

Up-regulate

1

R28

Ribulose-phosphate 3-epimerase

RL5P ↔ XUL5P

Up-regulate

1

R40

Isocitrate dehydrogenase (NADP+)

ICIT + NADP → AKG + CO2 + NADPH

Up-regulate

1

R39

Isocitrate dehydrogenase (NAD+)

ICITm + NADm → AKGm + CO2m + NADHm

Up-regulate

1

R725

5'-Nucleotidase

UMP + H₂O → PI + URI

Up-regulate

1

R137

Methylenetetrahydrofolate dehydrogenase (NAD+)

METTHF + NAD → METHF + NADH

Up-regulate

1

R38

Isocitrate dehydrogenase (NADP+)

ICITm + NADPm → AKGm + CO₂m + NADPHm

Up-regulate

1

R477

Argininosuccinate synthase

ASP + ATP + CITR → 2*H + AMP + PPI + ARGSUCC

Up-regulate

1

R238

Dihydroxyacetone synthase

XUL5P + FALD ↔ T3P1 + GLYN

Up-regulate

1

R376

4-Hydroxyphenylpyruvate dioxygenase

4HPP + O₂ → HOMOGEN + CO₂

Down-regulate

N/A

R78

Pyruvate decarboxylase

H + PYR → ACAL + CO₂

Up-regulate

N/A

R199

Aldehyde dehydrogenase (NAD+)

ACALm + NADm + H2Om → ACm + NADHm + 2*Hm

Down-regulate

N/A