Table 1

Reaction stoichiometry of the dynamic network model.

Stoichiometry


Reaction number

Reaction name

Substrates

Products


r1

glucokinase

GLCin + ATPin

G6Pin + ADPin + Hnb

r2

glucose-6-phosphate isomerase

G6Pin

F6Pin

r3

phosphofructokinase

F6Pin + ATPin

F16Pin + ADPin + Hnb

r4

fructose-bisphosphate aldolase

F16Pin

DHAPin + GAPin

r5

triose-phosphate isomerase

DHAPin

GAPin

r6

glyceraldehyde-3-phosphate dehydrogenase

GAPin + Pnb + NADin

13PGin + NADHin + Hnb

r7

phosphoglycerate kinase

13PGin + ADPin + Hnb

G3Pin + ATPin

r8

phosphoglycerate mutase

G3Pin

G2Pin

r9

pyruvate kinase

PEPin + ADPin + Hnb

PYRin + ATPin

r10

glucose-6-phosphate dehydrogenase

G6Pin + NADPin

GL6Pin + NADPHin + Hnb

r11

6-phosphogluconolactonase

GL6Pin + H2Onb

6GPin + Hnb

r12

phosphogluconate dehydrogenase

6GPin + NADPin

RIBU5Pin + CO2nb + NADPHin

r13

ribose-5-phosphate isomerase

RIBU5Pin

RIBO5Pin

r14

ribulose-phosphate 3-epimerase

RIBU5Pin

XYL5Pin

r15

transketolase

RIBO5Pin + XYL5Pin

GAPin + S7Pin

r16

transketolase

XYL5Pin + E4Pin

GAPin + F6Pin

r17

phosphopyruvate hydratase

G2Pin

PEPin + H2Onb + Hnb

r18

lactate dehydrogenase

PYRin + NADHin + Hnb

LACin + NADin

r19

adenosinetriphosphatase

ATPin + H2Onb

ADPin + Pnb + Hnb

r20

alanine transaminase

ALAin + AKGin

PYRin + GLUin

r21

phosphoglucomutase

G6Pin

G1Pin

r22

nadph consumption

NADPHin + Anb

NADPin + AHnb

r23

glycogen synthesis

UTPnb + G1Pin

UDPnb + GLYGnb + Hnb + PPnb

r24

transaldolase

S7Pin + GAPin

F6Pin + E4Pin

r25

adenylate kinase

ATPin + AMPin

2·ADPin

r26

glycerol synthesis

DHAPin

GLYCEROLnb

r27

nucleotide synthesis

RIBO5Pin + ATPin

PRPPin + AMPin + Hnb

r28

serine synthesis

G3Pin + NADin + GLUin + H2Onb

SERin + Pnb + NADHin + 2·Hnb + AKGin

r29

citrate synthase

OACin + ACCOAin + H2Onb

CITin + COAin + Hnb

r30

aconitate hydratase

CITin

CISACin + H2Onb

r31

aconitate hydratase

CISACin + H2Onb

ISOCITin

r32

isocitrate dehydrogenase

ISOCITin + NADin

AKGin + CO2nb + NADHin

r33

succinate-CoA ligase

SUCCOAin + Pnb + ADPin

SUCin + COAnb + ATPin

r34

fumarate hydratase

FUMin + H2Onb

MALin

r35

malate dehydrogenase

MALin + NADin

OACin + NADHin + Hnb

r36

pyruvate dehydrogenase complex

PYRin + NADin + COAnb

CO2nb + NADHin + ACCOAin

r37

alpha-ketoglutarate dehydrogenase complex

AKGin + NADin + COAnb

SUCCOAin + CO2nb + NADHin

r38

pyruvate synthesis

PYRnb

PYRin

r39

valine leucine isoleucine metabolism

ISOVALMETnb

SUCCOAin

r40

succinate dehydrogenase

SUCin + 0.6·NADin +0.2·O2nb

FUMin + 0.6·NADHin + 0.6·Hnb + 0.4·H2Oin

r41

oxidative phosphorylation

NADHin + 0.5·O2nb + 3.5·Hnb + 2.5·ADPin + 2.5·Pnb

NADin + 3.5·H2Onb + 2.5·ATPin

r42

alpha-ketoglutarate synthesis

AKGnb

AKGin

r43

malic enzyme

MALin + NADPin

PYRin + CO2nb + NADPHin

r44

glutamate dehydrogenase

GLUin + H2Onb + NADin

AKGin + NH4nb + NADHin + Hnb

r45

lactate transport

LACin

LACex

r46

pyruvate transport

PYRin

PYRex

r47

glucose transport

GLCin

GLCex

r48

alanine transport

ALAex

ALAin

r49

serine transport

SERin

SERin


The subscripts 'ex', 'in', and 'nb' denote extracellular, intracellular, and non-balanced metabolites, respectively.

The Phosphoenolpyruvate carboxykinase enzyme was found to be inactive in the reference state [7], and, thus, it was not included in the dynamic network model.

Maier et al. BMC Systems Biology 2010 4:54   doi:10.1186/1752-0509-4-54

Open Data