Download Table S1.

Table S1. Reactions found in the E. coli central metabolic network analyzed in this study
Reaction
ACCOA + OA --> COA + CIT
CIT --> OA + AC
MAL --> OA
CIT <--> ICIT
CIT <--> ICIT
ICIT + NADP <--> CO2 +
NADPH + AKG
AKG + NAD + COA --> CO2 +
NADH + SUCCOA
SUCCOA + ADP + PI <--> ATP
+ COA + SUCC
FUM <--> MAL
FUM <--> MAL
FUM <--> MAL
MAL + NAD --> NADH + OA
GLC + ATP --> G6P + ADP
G6P <--> F6P
F6P + ATP --> FDP + ADP
F6P + ATP --> FDP + ADP
FDP --> F6P + PI
FDP <--> T3P1 + T3P2
FDP <--> T3P1 + T3P2
FDP <--> T3P1 + T3P2
T3P2 <--> T3P1
T3P1 + PI + NAD <--> NADH +
13PDG
FDP --> F6P + PI
13PDG + ADP <--> 3PG + ATP
3PG <--> 2PG
3PG <--> 2PG
3PG <--> 2PG
2PG <--> PEP
PYR + ATP --> PEP + AMP + PI
PEP + ADP --> PYR + ATP
PEP + ADP --> PYR + ATP
PYR + COA + NAD --> NADH +
CO2 + ACCOA
G6P + NADP <--> D6PGL +
NADPH
D6PGL --> D6PGC
Protein/
protein
complex
GltA
CitDEF
Mqo
AcnA
AcnB
Description
b0720
b0615,b0616,b0617
b2210
b1276
b0118
Icd
b1136
LpdA and
SucAec and
SucBec
b0726,b0727,b0116
Frd
b0728,b0729
FumA
FumB
FumC
Mdh
Glk
Pgi
PfkA
PfkB
Fbp
FbaA
FbaB
B1773
Tpi
b1612
b4122
b1611
b3236
b2388
b4025
b3916
b1723
b4232
b2925
b2097
b1773
b3919
GapA
b1779
GlpX
Pgk
GpmB
GpmA
YibO
Eno
Ppsa
Pykf
Pyka
AceEec and
AceFec and
LpdA
b3925
b2926
b4395
b0755
b3612
b2779
b1702
b1676
b1854
ORFs
Citric acid cycle
Glycolysis/
gluconeogenesis
b0114,b0115,b0116
Zwf
b1852
PGL
b0767
Pentose
phosphate
pathway
D6PGC + NADP --> NADPH +
CO2 + RL5P
RL5P <--> R5P
RL5P <--> R5P
RL5P <--> X5P
RL5P <--> X5P
R5P + X5P <--> T3P1 + S7P
X5P + E4P <--> F6P + T3P1
T3P1 + S7P <--> E4P + F6P
R5P + X5P <--> T3P1 + S7P
X5P + E4P <--> F6P + T3P1
T3P1 + S7P <--> E4P + F6P
OA --> CO2 + PYR
ACCOA + 2 NADH <--> ETH +
2 NAD + COA
PYR + COA --> ACCOA + FOR
PYR + COA --> ACCOA + FOR
PYR + COA --> ACCOA + FOR
ACCOA + PI <--> ACTP + COA
ACCOA + PI <--> ACTP + COA
ACTP + ADP <--> ATP + AC
ACTP + ADP <--> ATP + AC
ACTP + ADP <--> ATP + AC
ATP + AC + COA --> AMP +
PPI + ACCOA
OA + ATP --> PEP + CO2 +
ADP
PEP + CO2 --> OA + PI
MAL + NADP --> CO2 +
NADPH + PYR
MAL + NAD --> CO2 + NADH
+ PYR
ICIT --> GLX + SUCC
ACCOA + GLX --> COA + MAL
ACCOA + GLX --> COA + MAL
PPI --> 2.00 PI
PPPI --> PI + PPI
PPI --> 2.00 PI
PPPI --> PI + PPI
PPI --> 2.00 PI
NADH + Q --> NAD + QH2 + 3
HEXT
NADH + Q --> NAD + QH2
FOR + Q --> QH2 + CO2 +
HEXT
FOR + Q --> QH2 + CO2 +
Gnd
b2029
RpiA
RpiB
Rpeec
SgcE
TktA
TktB
TalB
TalA
TktA
TktB
Eda
b2914
b4090
b3386
b4301
b2935
b2465
b0008
b2465
b2935
b2464
b1850
AdhE
b1241
PflC
TdcE
PflA
Pta
EutD
AckA
PurT
TdcD
b3951,b3952
b3114
b0902,b0903
b2297
b2458
b2296
b1849
b3115
Acs
b4069
Pck
b3403
Ppc
b3956
Mae
b2463
Sfc
b1479
AceA
AceB
GlcB
Ppa
PpxA
PpxB
SureEA
SureEB
Ndh
b4015
b4014
b2976
b4226
b2502
b2502
b2744
b2744
b2276,b2277,b2278
,b2279,b2280,b228
1,b2282,b2283,b22
84,b2285,b2286,b2
287,b2288
b1109
Fdoec
b3892,b3893,b3894
Fdn
b1474,b1475,b1476
Nuo
Pyruvate
metabolism
Anaplerotic
reactions
Oxidative
phosphorylation
HEXT
GL3P + Q --> T3P2 + QH2
GL3P + Q --> T3P2 + QH2
GlpD
GlpA
QH2 + 0.5 O2 --> Q + 2.5 HEXT
CyoA
PYR + NADH <--> NAD + LAC
PYR + NADH <--> NAD + LAC
LAC + Q --> 1 PYR + 1 QH2
QH2 + 0.5 O2 --> Q + 2 HEXT
NADPH + Q --> NADP + QH2
PYR + Q --> AC + CO2 + QH2
QH2 + 0.5 O2 --> Q + 4 HEXT
NADPH + NAD --> NADP +
NADH
NADP + NADH + 2 HEXT <-->
NADPH + NAD
Dld
Ldh
Dld
CbdAB
MdaB
PoxB
CydA
b3426
b2241,b2242,b2243
b0429,b0430,b0431
,b0432
b2133
b1380
b2133
b0978,b0979
b0978,b0979
b0871
b0733,b0734
Pnt
b1602,b1603
SthA
b3962
ATP --> ADP + PPPI
ATP + PI --> ADP + PPI
NADPH + NAD --> NADP +
NADH
PpkA
PpkB
b3736,b3737,b3738
,b3731,b3732,b373
3,b3734,b3735,b37
39
b2501
b2501
SthA
b3962
SUCC + Q --> QH2 + FUM
Sdh
b0721,b0722,b0723
,b0724
O2xt <--> O2
CO2xt <--> CO2
ATP --> ADP + PI
LCTS --> GLC + bDGLAC
LCTS --> GLC + bDGLAC
bDGLAC <--> GLAC
bDGLC <--> GLC
GLAC + ATP <--> GAL1P +
ADP
GAL1P + UTP <--> PPI +
UDPGAL
GL + ATP --> ADP + GL3P
GL3P + NADP <--> T3P2 +
NADPH
RIB + ATP --> R5P + ADP
UDPGAL <--> UDPG
UTP + G1P <--> PPI + UDPG
G1P <--> G6P
G1P <--> G6P
O2TXR
CO2TXR
ATPM
LacZ
BglX
GALM1R
GALM2R
b0344
b2132
b0756
b0756
GalK
b0757
GalT
b0758
GlpK
b3926
GpsA
b3608
RbsK
GalE
GalUec
Pgmec
YqaB
b3752
b0759
b1236
b0688
b2690
ATP + AMP --> 2 ADP
Adk
b0474
ATP <--> ADP + PI + 4 HEXT
41.25 ATP + 3.54 NAD + 18.22
AtpF0, AtpF1,
AtpI
Alternate carbon
metabolism and
related reactions
Nucleotide
Salvage
Pathway
Biomass
NADPH + 0.20 G6P + 0.07 F6P +
0.89 R5P + 0.36 E4P + 0.12 T3P1
+ 1.49 3PG + 0.51 PEP + 2.83
PYR + 3.74 ACCOA + 1.78 OA -> 3.74 COA + 1.07 AKG + 41.25
ADP + 41.250 PI + 3.54 NADH +
18.22 NADP + Biomass
Biomass + 41.25 ATP --> 41.25
ADP + 41.25 PI
Transport reactions
reaction
Growth
FORxt <--> FOR
FocA
b0904
LCTSxt + HEXT <--> LCTS
LacY
b0343
FORxt <--> FOR
FocB
b2492
ETHxt + HEXT <--> ETH
ETHUPR
SUCCxt + HEXT <--> SUCC
DctA
b3528
SUCCxt + HEXT <--> SUCC
DcuB
b4123
SUCCxt + HEXT <--> SUCC
DcuA
b4138
SUCC --> SUCCxt + HEXT
DcuC
b0621
PYRxt + HEXT <--> PYR
PYRUPR
PIxt + HEXT <--> PI
PitA
b3493
PIxt + HEXT <--> PI
PitBec
b2987
GLCxt + HEXT --> GLC
GalP
b2943
G6Pxt + HEXT --> G6P
UhpT
b3666
Formate
transport via
diffusion
Lactose
transport via
proton symport
Formate
transport via
diffusion
Succinate
transport via
proton symport
2H
Succintate
transport via
proton symport
3H
Succintate
transport via
proton symport
3H
Succintate
transport via
proton symport
3H
Phosphate
reversible
transport via
symport
Phosphate
reversible
transport via
symport
Glucose
transport in via
proton symport
Glucose 6
phosphate
GLCxt + PEP --> G6P + PYR
GLCxt + PEP --> G6P + PYR
GLCxt + PEP --> G6P + PYR
Crr and PtsG
and PtsH and
PtsI
Crr and MalX
and PtsH and
PtsI
ManX and
ManY and
ManZ and PtsH
and PtsI
b2417,b1101,b2415
,b2416
b2417,b1621,b2415
,b2416
b1817,b1818,b1819
,b2415,b2416
GLxt --> GL
GlpF
b3927
RIBxt + ATP --> RIB + ADP + PI
RbsA and RbsB
and RbsC and
RbsDec
b3749+b3751+b37
50
ACxt + HEXT <--> AC
ACUPR
b4067
LAC <--> LACxt + HEXT
LldP
b3603
LAC <--> LACxt + HEXT
GlcA
b2975
GLCxt <-->
G6Pxt <-->
RIBxt <-->
GLxt <-->
SUCCxt <-->
PYRxt <-->
LACxt <-->
LCTSxt <-->
FORxt <-->
transport via
phosphate
antiport
Glucose
transport via
PEPPyr PTS
Glucose
transport via
PEPPyr PTS
Glucose
transport via
PEPPyr PTS
Glycerol
transport via
channel
Ribose transport
via ABC system
Acetate
reversible
transport via
proton symport
Lactate
reversible
transport via
proton symport
Lactate
reversible
transport via
proton symport
Glucose
exchange
Glucose 6
phophate
exchange
Ribose
exchange
Glycerol
exchange
Succinate
exchange
Pyruvate
exchange
Lactate
exchange
Lactose
exchange
Formate
exchange
Ethanol
exchange
Acetate
exchange
Phosphate
exchange
Carbon dioxide
exchange
Oxygen
exchange
ETHxt <-->
ACxt <-->
PIxt <-->
CO2xt <-->
O2xt <-->
Note that reactions catalyzed by more than one protein/protein complex are listed multiple times. The data are based
on information published in Covert et al. (Bioinformatics 24:2044, 2008) and the most recent reconstruction
(denoted by iAF1260) of the E. coli metabolic network (see Feist et al., Mol Sys Biol 3:121, 2007;
http://gcrg.ucsd.edu/In_Silico_Organisms/E_coli/E_coli_SBML).
Metabolite
names:
13PDG
1,3-bis-
phosphoglycerate; 2PG 2-phosphoglycerate; 3PG 3-phosphoglycerate; AC acetate; ACCOA acetyl CoA; ACTP
acetyl phosphate; ACxt acetate; ADP adenosine diphosphate; AKG alpha ketoglutaric acid; AMP adenosine
monophosphate; ATP adenosine triphosphate; CIT citrate; CO2 carbon dioxide; CO2xt carbon dioxide, external;
COA coenzyme A; D6PGC D-6-phosphogluconate; D6PGL D-6-phosphogluconolactone; E4P D-erythrose-4phosphate; ETH ethanol; F6P fructose-6-phosphate; FDP fructose-1,6-biphosphate; FOR formic acid; FUM fumaric;
G1P glucose-1-phosphate; G6P glucose-6-phosphate; G6Pxt glucose-6-phosphate, external; GAL1P galactose-1phosphate; GL glycerol; GL3P glycerol-3-phosphate; GLAC galactose; GLC glucose; GLX glyoxylate; HEXT
external H+; ICIT iso-citric acid; LAC D-lactate; LCTS Lactose; MAL maltose; NAD nicotinamide adenine
dinucleotide; NADH nicotinamide adenine dinucleotide, reduced; NADP nicotinamide adenine dinucleotide
phosphate; NADPH nicotinamide adenine dinucleotide phosphate, reduced; O2 oxygen; OA oxaloacetate; PEP
phosphoenolpyruvate; PI phosphate; PPI pyrophosphoric acid; PPP inorganic triphosphate; PYR pyruvate; Q
ubiquinone; QH2 ubiquinol; R5P ribose-5-phosphate; RIB ribose; RL5P ribulose-5-phosphate; S7P sedo heptulose;
SUCC succinate; SUCCOA succinyl CoA; T3P1 glyceraldehyde-3-phosphate; T3P2 dihydroxyacetone phosphate;
UDPG uridine diphosphate glucose; UDPGAL uridine diphosphate galactose; UTP uridine triphosphate; X5P
xylulose-5-phosphate; bDGLAC beta-D-galactose; bDGLC beta-D-glucose. Additional abbreviations: ex exchange;
xt extracellular.