Supplementary Data Sheet 4: Model Results – Central Metabolism of Escherichia coli
coa
0 50 100 150
1.
40
1.
55
accoa
0 50 100 1500
.0
0
0.
15
succoa
0 50 100 150
1.
05
1.
15
glc-D(e)
0 50 100 1500.
0e
+0
0
2.
0e
−0
5
glc-D
0 50 100 1504.
0e
−0
7
1.
2e
−0
6
g6p
0 50 100 1500
.0
0
0.
15
l
l
l
l
l
l
ll
l
l
f6p
0 50 100 1500
.0
0
0.
15
l l l
llll
l
fdp
0 50 100 1500
.0
00
0.
02
5
l
l
l lll
l
l
g3p
0 50 100 1500
.0
0
0.
03
dhap
0 50 100 150
0.
0
0.
4
0.
8
13dpg
0 50 100 1500
.0
0
0.
03
3pg
0 50 100 1500
.0
0
0.
20
l
l l
ll
ll
ll
2pg
0 50 100 1500
.0
00
0.
02
5
pep
0 50 100 1500
.0
0
0.
10
l
l l
l
l
l
ll
ll
pyr
0 50 100 150
0.
0
1.
0
2.
0
l
l l
l
l
ll
l
l
l
accoa
0 50 100 1500
.0
0
0.
15
for
0 50 100 150
0.
01
0.
04
l
l
l
l
l
l
l l
h2
0 50 100 150
0.
00
5
0.
01
5
lac
0 50 100 1500
e+
00
4e
−0
4
cit
0 50 100 1500.
00
00
0.
00
20
l
l l
l
l
ll
l
l
icit
0 50 100 1500
e+
00
8e
−0
5
l
l l
l
ll
ll
l
akg
0 50 100 150
0.
0
1.
0
2.
0
succoa
0 50 100 150
1.
05
1.
15
succ
0 50 100 150
0
4
8
l
l
l
l
l
l
l
l
l
fum
0 50 100 150
0.
0
1.
0 l
l
l
ll
l
l
l
l
mal
0 50 100 150
0
2
4
6
l
l l
ll
l
l
l
l
l
oaa
0 50 100 1500
.0
0
0.
03
actp
0 50 100 150
0.
00
2
0.
01
2
ac
0 50 100 150
0.
05
0.
25
ac(e)
0 50 100 150
0.
00
5
0.
02
0
etoh
0 50 100 1500
.0
0
0.
15
etoh(e)
0 50 100 1500
.0
00
0.
01
5
glx
0 50 100 1500
.0
00
0.
01
5
o2(e)
0 50 100 1500
e+
00
8e
−0
6
q8h2
0 50 100 150
0.
0
1.
5
l
l
l l
l
q8
0 50 100 150
0.
0
1.
5
3.
0
l
l
l l l l l
l
nadh
0 50 100 150
0.
0
0.
4
0.
8
nad
0 50 100 150
0
2
4
mql8
0 50 100 150
0.
0
0.
2
0.
4
mqn8
0 50 100 150
0.
0
1.
0
2.
0
nadh
0 50 100 150
0.
0
0.
4
0.
8
nad
0 50 100 150
0
2
4
nadph
0 50 100 150
0.
4
1.
0
nadp
0 50 100 150
1.
4
2.
0
6pgl
0 50 100 1501.
0e
−1
0
4.
5e
−1
0 6pgc
0 50 100 1500
.0
00
10
r5p
0 50 100 1500
.0
00
0.
00
4
l l
l l
l
l
ll
ru5p
0 50 100 1500
.0
00
6
0.
00
16
xu5p
0 50 100 1500.
00
10
0.
00
30
s7p
0 50 100 1502
e−
04
6e
−0
4
e4p
0 50 100 1503
e−
05
9e
−0
5
2ddg6p
0 50 100 1500
.0
00
0.
00
4
FNR
0 50 100 150
0.
0
0.
6
ArcA
0 50 100 150
0.
0
0.
6
1.
2
CRP
0 50 100 150
0.
0
0.
6
FruR
0 50 100 150
0.
0
0.
6
PdhR
0 50 100 150
0.
0
0.
6
AppY
0 50 100 150
0.
0
0.
6
IclR
0 50 100 150
0.
3
0.
7
FDH-H
0 50 100 150
0
10
25
FDH-N
0 50 100 1500
.0
00
0.
01
5
FDH-O
0 50 100 1500
.0
00
0.
01
5
FORt
0 50 100 150
0
2
4
6
ll
l
l
l
l
l
l
l
l
llll lll l l
H2t
0 50 100 150
0
10
20
CYTBO3
0 50 100 150
0
2
4
6
CYTBD
0 50 100 150
0
2
4
6
CYTBD2
0 50 100 150
0
2
4
6
NUO(q8)
0 50 100 150
0
5
10
NDH(q8)
0 50 100 150
0
10
20
NUO(mqn)
0 50 100 150
−
2.
0
0.
0
ATPS
0 50 100 150
−
5
10
25
ADK
0 50 100 1500
.0
10
0.
03
5
PPA
0 50 100 150
0.
00
5
nadph %
0 50 100 150
0
40
80
[%
]
THD-SthA
0 50 100 150
0.
2
0.
5
0 50 100 150
0.
04
0.
12
G6PDH2r
0 50 100 150
0
2
4
PGL
0 50 100 150
1.
0
2.
5
GND
0 50 100 150
0.
0
1.
5
3.
0
RPE
0 50 100 150
0.
05
0.
25
RPI
0 50 100 150
−
0.
35
TALA
0 50 100 150
0.
10
0.
20
TKT1
0 50 100 150
0.
10
0.
20
TKT2
0 50 100 150
0.
00
0.
10
EDA
0 50 100 150
1.
0
2.
0
EDD
0 50 100 150
1.
0
2.
0
SUCCex
0 50 100 150
0.
0
2.
0
ll
ll l l
ll
llll lll l l
GLCpts
0 50 100 150
0.
0
1.
0
GLCabc
0 50 100 150
2
6
10
HEX1
0 50 100 150
2
6
10
PGI
0 50 100 150
2
6
PFK
0 50 100 150
2
6
10
FBA
0 50 100 150
2
6
10
TPI
0 50 100 150
2
6
10
GAPD
0 50 100 150
5
15
PGK
0 50 100 150
−
20
−
10
PGM
0 50 100 150
−
20
−
10
ENO
0 50 100 150
5
15
PYK
0 50 100 150
0
10
25
PPS
0 50 100 150
0.
01
0.
04
PDH
0 50 100 150
0
2
4
PFL
0 50 100 150
0
10
25
CS
0 50 100 150
0
2
4
ACONT
0 50 100 150
0
2
4
ICDHyr
0 50 100 150
0.
5
2.
0
AKGDH
0 50 100 150
0.
0
1.
5
SUCOAS
0 50 100 150−
2.
5
−
1.
0
SUCDH
0 50 100 150
0.
0
0.
2
0.
4
FRD
0 50 100 150−
1.
0
1.
0
FUM
0 50 100 150
−
0.
5
1.
5
MDH
0 50 100 150
−
0.
5
1.
5
MQO(q8)
0 50 100 1500
.0
00
0.
00
6
MQO(mqn)
0 50 100 150
0.
04
0.
10
ACS
0 50 100 1500
.0
0
0.
03
LDH
0 50 100 150−7
e−
07
0e
+0
0
POX
0 50 100 1500
e+
00
4e
−0
4
PTAr
0 50 100 150
0
4
8
14
ACKr
0 50 100 150
−
10
−
4
0
ACt
0 50 100 150
0
4
8 l
lll l
l ll
llll
lll l l
LACt
0 50 100 150
0
4
8
l l l ll llll lll l l
ADHEr
0 50 100 150
0
4
8
ETOHt
0 50 100 150
0
4
8 ll
ll
l
l
l
ll
llll lll l l
PPC
0 50 100 150
2
6
12
PPCK
0 50 100 150
0
4
8
14
ICL
0 50 100 150
0.
0
0.
3
MALS
0 50 100 150
0.
0
0.
3
ATPM
0 50 100 150
0
5
15
nadh %
0 50 100 150
0
20
40
[%
]
q82 %
0 50 100 150
0
40
80
[%
]
ll l l
l l l l
l
l
q8 total
0 50 100 150
0
2
4
l
l
l l
l
l l
ll
nad total
0 50 100 150
0
2
4
nadh %
0 50 100 150
0
20
40
[%
]
mql8 %
0 50 100 150
0
40
80
[%
]
mq total
0 50 100 1500
.0
1.
0
2.
0
l
l l l l
l l
nad total
0 50 100 150
0
2
4
O2t
0 50 100 150
0
5
15
CO2t
0 50 100 150
0
10
20
lll
l
l l ll
l
lll lll
l l
Energy Charge
0 50 100 150
50
70
90
[%
]
Yield
0 50 100 150
0
40
80
Y G
lc
 
[g 
m
o
l−1
]
1.
40
1.
55
0.
00
0.
15
1.
05
1.
15
0.
0e
+0
0
2.
0e
−0
5
4.
0e
−0
7
1.
2e
−0
6
0.
00
0.
15
0.
00
0.
15
0.
00
0
0.
02
5
0.
00
0.
03
0.
0
0.
4
0.
8
0.
00
0.
03
0.
00
0.
20
0.
00
0
0.
02
5
0.
00
0.
10
0.
0
1.
0
2.
0
0.
00
0.
15
0.
01
0.
04
0.
00
5
0.
01
5
0e
+0
0
4e
−0
4
0.
00
00
0.
00
20
0e
+0
0
8e
−0
5
0.
0
1.
0
2.
0
1.
05
1.
15
0
4
8
0.
0
1.
0
0
2
4
6
0.
00
0.
03
0.
00
2
0.
01
2
0.
05
0.
25
0.
00
5
0.
02
0
0.
00
0.
15
0.
00
0
0.
01
5
0.
00
0
0.
01
5
0e
+0
0
8e
−0
6
0.
0
1.
5
0.
0
1.
5
3.
0
0.
0
0.
4
0.
8
0
2
4
0.
0
0.
2
0.
4
0.
0
1.
0
2.
0
0.
0
0.
4
0.
8
0
2
4
0.
4
1.
0
1.
4
2.
0
1.
0e
−1
0
4.
5e
−1
0
0.
00
01
0
0.
00
0
0.
00
4
0.
00
06
0.
00
16
0.
00
10
0.
00
30
2e
−0
4
6e
−0
4
3e
−0
5
9e
−0
5
0.
00
0
0.
00
4
0.
0
0.
6
0.
0
0.
6
1.
2
0.
0
0.
6
0.
0
0.
6
0.
0
0.
6
0.
0
0.
6
0.
3
0.
7
Legend: Steady-state simulation results of the model in comparison to measurement data. The abscissa is aerobiosis in percent.
White boxes represent metabolites. The ordinate is in nmol/g. Blue lines and circles show simulation and measurement data, respectively. The error bars show the technical
standard deviation.
Gray boxes represent reactions. The blue lines show the reaction flux in mmol/gDCW/h. Blue symbols show flux data computed from the steady state concentration of
extracellular concentrations. Different symbols indicate that the data was measured in different laboratories. The red lines show gene expression in arbitrary units. If two red lines
are shown, they refer to different genes with qualitatively different expression. Red triangles show microarray data. If for one reaction several triangles are shown, they refer to
different genes. Red squares show RT-PCR data with standard deviation.
The labels of the boxes are explained in Supplementary Data Sheet 1
Michael Ederer SysMO-SUMO