Table S2. Grouped reactions for central metabolism of Escherichia coli by genomic context and flux-converging pattern analyses
Group* / Reaction / Gene / CxJyƗ(Glucose) / Enzyme / Metabolism / EC number
1 / ICL / aceA / C6JCE/C6JDE / Isocitrate lyase / Anaplerotic pathway / 4.1.3.1
MALS / glcB
aceB / C2JCE/C2JDE / malate synthase / Anaplerotic pathway / 4.1.3.2
2 / ACONT / acnA
acnB / C6JCE/C6JDE
/C6JB / aconitase / TCA Cycle / 4.2.1.3
CS / gltA / C6JCE/C6JDE
/C6JB / citrate synthase / TCA Cycle / 4.1.3.7
ICDHyr / icd / C6JCE/C6JDE
/C6JB / isocitrate dehydrogenase (NADP) / TCA Cycle / 1.1.1.42
3 / FRD2~3 / frdA
frdB
frdC
frdD / C4JC / fumarate reductase / TCA Cycle / 1.3.99.1
TEST_AKGDH / sucA
sucB
lpd / C5JCE/C5JDE
/C5JB / 2-Oxogluterate dehydrogenase / TCA Cycle
MDH / mdh / C4JDE/ C4JC (C4JB) / malate dehydrogenase / TCA Cycle / 1.1.1.37
SUCD1i / sdhA
sdhB
sdhC
sdhD / C4JCE/C4JDE
/C4JB / succinate dehydrogenase / TCA Cycle / 1.3.99.1
SUCOAS / sucC
sucD / C4JCE/C4JDE
/C4JB / succinyl-CoA synthetase (ADP-forming) / TCA Cycle / 6.2.1.5
PDH / aceE
aceF
lpd / C3JCE/C3JDE / pyruvate dehydrogenase / Glycolysis
4 / ENO / eno / C3JB / enolase / Glycolysis / 4.2.1.11
GAPD / gapA
gapC / C3JB / glyceraldehyde-3-phosphate dehydrogenase / Glycolysis / 1.2.1.12
PGM / pgmI
gpmA
gpmB / C3JB / phosphoglycerate mutase / Glycolysis / 5.4.2.1
PFK / pfkA
pfkB / C6JA / phosphofructokinase / Glycolysis / 2.7.1.11
PGK / pgk / C3JB / phosphoglycerate kinase / Glycolysis / 2.7.2.3
PYK / pykF
pykA / C3JB / pyruvate kinase / Glycolysis / 2.7.1.40
TPI / tpi / C3JA / triose-phosphate isomerase / Glycolysis / 5.3.1.1
5 / GLK / glk / C6JA / glucokinase / Glycolysis / 2.7.1.1
PGI / pgi / C6JA / glucose-6-phosphate isomerase / Glycolysis / 5.3.1.9
EDA / eda / C6JA / 2-dehydro-3-deoxy-phosphogluconate aldolase / Entner-Doudoroff pathway / 4.1.2.14
EDD / edd / C6JA / 6-phosphogluconate dehydratase / Entner-Doudoroff pathway
GND / gnd / C6JA / phosphogluconate dehydrogenase / Pentose Phosphate pathway / 1.1.1.44
G6PDH2r / zwf / C6JA / glucose 6-phosphate dehydrogenase / Pentose Phosphate pathway / 1.1.1.49
6 / RPE / rpe
sgcE / C5JA / ribulose 5-phosphate 3-epimerase / Pentose Phosphate pathway / 5.1.3.1
TALA / talA
talB / C10JA / transaldolase / Pentose Phosphate pathway / 2.2.1.2
TKT1 / tktA
tktB / C10JA / transketolase / Pentose Phosphate pathway / 2.2.1.1
TKT2 / tktA
tktB / C9JA / transketolase / Pentose Phosphate pathway / 2.2.1.1
7 / ACKr / ack
purT / C2JCE/C2JDE / acetate kinase / Pyruvate metabolism / 2.7.2.1
PTAr / pta
eutD / C2JCE/C2JDE / phosphotransacetylase / Pyruvate metabolism / 2.3.1.8
8 / ADHEr / adhE / C2JCE/C2JDE / Acetaldehyde dehydrogenase / Pyruvate metabolism
PFL / pflA
pflB
pflC
pflD
tdcE / C3JCE/C3JDE / pyruvate formate lyase / Pyruvate metabolism
9 / GLCS1 / glgA / C6JA / glycogen synthase (ADPGlc) / Glycolysis / 2.4.1.21
GLGC / glgC / C6JA / glucose-1-phosphate adenylyltransferase / Glycolysis / 2.7.7.27
GLCP / glgP
malP / C6JA / glycogen phosphorylase / Glycolysis / 2.4.1.1
*Each group was created by three types of genomic context analyses, namely the conserved neighborhood, gene fusion and co-occurrence. The conserved neighborhood captures genes in proximity of one another on genome, which repeatedly occur across organisms. The gene fusion captures events of forming a hybrid gene from previously separate genes per organisms, and the co-occurrence predicts presence or absence of linked proteins across organisms. Reactions in the same group were subjected to the same on/off constraints.
ƗThen, reactions in each group were further clustered based on flux-converging analysis, in which the number of carbons (Cx) in reaction-participating metabolites and the number of passing flux-converging metabolites of metabolic fluxes from the given carbon source (Jy); reactions having the consistent CxJy were assigned to the same set. Reactions in the same sets were constrained in a consistent manner, such that they were forced to have similar scale of flux values. The parenthesis indicates the CxJy of reverse reaction.
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