Skip to content

Commit 9dd431e

Browse files
pierremillardpierremillard
committed
Create e_coli_13C_noxch.r
1 parent 54ebbde commit 9dd431e

File tree

1 file changed

+196
-0
lines changed

1 file changed

+196
-0
lines changed

‎e_coli_13C_noxch.r‎

Lines changed: 196 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,196 @@
1+
# 2014-28-08 millard@insa-toulouse.fr
2+
#
3+
# Model of the glycolytic and pentose phosphate pathways of E. coli
4+
# published in the following paper:
5+
#
6+
# Impact of kinetic isotope effects in isotope labeling experiments
7+
# by P. Millard, S. Sokol, J.C. Portais and P. Mendes
8+
#
9+
# A graphical representation of this network in SBGN format can be
10+
# found in Figure 2 of the paper.
11+
#
12+
# 'rxn' : list containing the topology of the metabolic network, the
13+
# carbon atom transitions, and the rate laws
14+
# 'kp' : named vector of parameters
15+
#
16+
# note: in this version, reversible reactions are not converted to two
17+
# irreversible reactions, hence isotope exchange between
18+
# metabolite pools is not taken into account
19+
#
20+
# Copyright 2014, INRA, France
21+
# License: GNU General Public License v2 (see license.txt for details)
22+
23+
# network definition
24+
# reaction substrate(s) product(s) carbon atom transitions rate law
25+
rxn=list('PTS'= list('su'=c('GLC','PEP'), 'pr'=c('G6P','PYR'), 'tr'=c('abcdef','ghi','abcdef','ghi'), 'eq'="65*PTSrmaxPTS*GLC*(PEP/PYR)/((PTSKPTSa1+PTSKPTSa2*(PEP/PYR)+PTSKPTSa3*GLC+GLC*(PEP/PYR))*(1+G6P**PTSnPTSg6p/PTSKPTSg6p))"),
26+
'PGI'= list('su'=c('G6P',''), 'pr'=c('F6P',''), 'tr'=c('abcdef','','abcdef',''), 'eq'="PGIrmaxPGI*(G6P-F6P/PGIKPGIeq)/(PGIKPGIg6p*(1+F6P/(PGIKPGIf6p*(1+PGN/PGIKPGIf6ppginh))+PGN/PGIKPGIg6ppginh)+G6P)"),
27+
'GPM'= list('su'=c('G6P',''), 'pr'=c('G1P',''), 'tr'=c('abcdef','','abcdef',''), 'eq'="PGMrmaxPGM*(G6P-G1P/PGMKPGMeq)/(PGMKPGMg6p*(1+G1P/PGMKPGMg1p)+G6P)"),
28+
'G6PDH'= list('su'=c('G6P',''), 'pr'=c('PGN',''), 'tr'=c('abcdef','','abcdef',''), 'eq'="G6PDHrmaxG6PDH*G6P*cnadp/((G6P+G6PDHKG6PDHg6p)*(1+cnadph/G6PDHKG6PDHnadphg6pinh)*(G6PDHKG6PDHnadp*(1+cnadph/G6PDHKG6PDHnadphnadpinh)+cnadp))"),
29+
'PFK'= list('su'=c('F6P',''), 'pr'=c('FBP',''), 'tr'=c('abcdef','','abcdef',''), 'eq'="PFKrmaxPFK*catp*F6P/((catp+PFKKPFKatps*(1+cadp/PFKKPFKadpc))*(F6P+PFKKPFKf6ps*(1+PEP/PFKKPFKpep+cadp/PFKKPFKadpb+camp/PFKKPFKampb)/(1+cadp/PFKKPFKadpa+camp/PFKKPFKampa))*(1+PFKLPFK/(1+F6P*(1+cadp/PFKKPFKadpa+camp/PFKKPFKampa)/(PFKKPFKf6ps*(1+PEP/PFKKPFKpep+cadp/PFKKPFKadpb+camp/PFKKPFKampb)))**PFKnPFK))"),
30+
'TA'= list('su'=c('GAP','S7P'), 'pr'=c('F6P','E4P'), 'tr'=c('abc','defghij','defabc','ghij'), 'eq'="TArmaxTA*(GAP*S7P-E4P*F6P/TAKTAeq)"),
31+
'TK1'= list('su'=c('R5P','X5P'), 'pr'=c('GAP','S7P'), 'tr'=c('abcde','fghij','cde','abfghij'), 'eq'="TK1rmaxTKa*(R5P*X5P-S7P*GAP/TK1KTKaeq)"),
32+
'TK2'= list('su'=c('E4P','X5P'), 'pr'=c('GAP','F6P'), 'tr'=c('abcd','efghi','ghi','efabcd'), 'eq'="TK2rmaxTKb*(X5P*E4P-F6P*GAP/TK2KTKbeq)"),
33+
'MURSYN'= list('su'=c('F6P',''), 'pr'=c('',''), 'tr'=c('abcdef','','',''), 'eq'="MURSYNv*2"),
34+
'ALD'= list('su'=c('FBP',''), 'pr'=c('DHAP','GAP'), 'tr'=c('abcdef','','cba','def'), 'eq'="ALDrmaxALDO*(FBP-GAP*DHAP/ALDkALDOeq)/(ALDkALDOfdp+FBP+ALDkALDOgap*DHAP/(ALDkALDOeq*ALDVALDOblf)+ALDkALDOdhap*GAP/(ALDkALDOeq*ALDVALDOblf)+FBP*GAP/ALDkALDOgapinh+GAP*DHAP/(ALDVALDOblf*ALDkALDOeq))"),
35+
'GAPDH'= list('su'=c('GAP',''), 'pr'=c('BPG',''), 'tr'=c('abc','','abc',''), 'eq'="GAPDHrmaxGAPDH*(GAP*cnad-BPG*cnadh/GAPDHKGAPDHeq)/((GAPDHKGAPDHgap*(1+BPG/GAPDHKGAPDHpgp)+GAP)*(GAPDHKGAPDHnad*(1+cnadh/GAPDHKGAPDHnadh)+cnad))"),
36+
'TPI'= list('su'=c('DHAP',''), 'pr'=c('GAP',''), 'tr'=c('abc','','cba',''), 'eq'="TPIrmaxTIS*(DHAP-GAP/TPIkTISeq)/(TPIkTISdhap*(1+GAP/TPIkTISgap)+DHAP)"),
37+
'GDH'= list('su'=c('DHAP',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="GDHrmaxG3PDH*DHAP/(GDHKG3PDHdhap+DHAP)"),
38+
'PGK'= list('su'=c('BPG',''), 'pr'=c('PG3',''), 'tr'=c('abc','','abc',''), 'eq'="PGKrmaxPGK*(cadp*BPG-catp*PG3/PGKKPGKeq)/((PGKKPGKadp*(1+catp/PGKKPGKatp)+cadp)*(PGKKPGKpgp*(1+PG3/PGKKPGKpg3)+BPG))"),
39+
'SERSYN'= list('su'=c('PG3',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="SERSYNrmaxSerSynth*PG3/(SERSYNKSerSynthpg3+PG3)"),
40+
'PGM'= list('su'=c('PG3',''), 'pr'=c('PG2',''), 'tr'=c('abc','','abc',''), 'eq'="PGMrmaxPGluMu*(PG3-PG2/PGMKPGluMueq)/(PGMKPGluMupg3*(1+PG2/PGMKPGluMupg2)+PG3)"),
41+
'ENO'= list('su'=c('PG2',''), 'pr'=c('PEP',''), 'tr'=c('abc','','abc',''), 'eq'="ENOrmaxENO*(PG2-PEP/ENOKENOeq)/(ENOKENOpg2*(1+PEP/ENOKENOpep)+PG2)"),
42+
'PYK'= list('su'=c('PEP',''), 'pr'=c('PYR',''), 'tr'=c('abc','','abc',''), 'eq'="PYKrmaxPK*PEP*(PEP/PYKKPKpep+1)**(PYKnPK-1)*cadp/(PYKKPKpep*(PYKLPK*((1+catp/PYKKPKatp)/(FBP/PYKKPKfdp+camp/PYKKPKamp+1))**PYKnPK+(PEP/PYKKPKpep+1)**PYKnPK)*(cadp+PYKKPKadp))"),
43+
'PPC'= list('su'=c('PEP',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="PPCrmaxpepCxylase*PEP*(1+(FBP/PPCKpepCxylasefdp)**PPCnpepCxylasefdp)/(PPCKpepCxylasepep+PEP)"),
44+
'SYN1'= list('su'=c('PEP',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="SYN1rmaxSynth1*PEP/(SYN1KSynth1pep+PEP)"),
45+
'SYN2'= list('su'=c('PYR',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="SYN2rmaxSynth2*PYR/(SYN2KSynth2pyr+PYR)"),
46+
'DAHPSYN'= list('su'=c('E4P','PEP'), 'pr'=c('',''), 'tr'=c('abcd','efg','',''), 'eq'="DAHPSYNrmaxDAHPS*E4P**DAHPSYNnDAHPSe4p*PEP**DAHPSYNnDAHPSpep/((DAHPSYNKDAHPSe4p+E4P**DAHPSYNnDAHPSe4p)*(DAHPSYNKDAHPSpep+PEP**DAHPSYNnDAHPSpep))"),
47+
'PDH'= list('su'=c('PYR',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="PDHrmaxPDH*PYR**PDHnPDH/(PDHKPDHpyr+PYR**PDHnPDH)"),
48+
'GND'= list('su'=c('PGN',''), 'pr'=c('RB5P',''), 'tr'=c('abcdef','','abcde',''), 'eq'="GNDrmaxPGDH*PGN*cnadp/((PGN+GNDKPGDHpg)*(cnadp+GNDKPGDHnadp*(1+cnadph/GNDKPGDHnadphinh)*(1+catp/GNDKPGDHatpinh)))"),
49+
'RPI'= list('su'=c('RB5P',''), 'pr'=c('R5P',''), 'tr'=c('abcde','','abcde',''), 'eq'="RPIrmaxR5PI*(RB5P-R5P/RPIKR5PIeq)"),
50+
'RPE'= list('su'=c('RB5P',''), 'pr'=c('X5P',''), 'tr'=c('abcde','','abcde',''), 'eq'="RPErmaxRu5P*(RB5P-X5P/RPEKRu5Peq)"),
51+
'RPP'= list('su'=c('R5P',''), 'pr'=c('',''), 'tr'=c('abcde','','',''), 'eq'="RPPrmaxRPPK*R5P/(RPPKRPPKrib5p+R5P)"),
52+
'G1PAT'= list('su'=c('G1P',''), 'pr'=c('',''), 'tr'=c('abcdef','','',''), 'eq'="G1PATrmaxG1PAT*G1P*catp*(1+(FBP/G1PATKG1PATfdp)**G1PATnG1PATfdp)/((G1PATKG1PATatp+catp)*(G1PATKG1PATg1p+G1P))"),
53+
'G6Pdilution'= list('su'=c('G6P',''), 'pr'=c('',''), 'tr'=c('abcdef','','',''), 'eq'="mu*G6P"),
54+
'F6Pdilution'= list('su'=c('F6P',''), 'pr'=c('',''), 'tr'=c('abcdef','','',''), 'eq'="mu*F6P"),
55+
'FDPdilution'= list('su'=c('FBP',''), 'pr'=c('',''), 'tr'=c('abcdef','','',''), 'eq'="mu*FBP"),
56+
'GAPdilution'= list('su'=c('GAP',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="mu*GAP"),
57+
'DHAPdilution'= list('su'=c('DHAP',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="mu*DHAP"),
58+
'BPGdilution'= list('su'=c('BPG',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="mu*BPG"),
59+
'PG3dilution'= list('su'=c('PG3',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="mu*PG3"),
60+
'PG2dilution'= list('su'=c('PG2',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="mu*PG2"),
61+
'PEPdilution'= list('su'=c('PEP',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="mu*PEP"),
62+
'RB5Pdilution'= list('su'=c('RB5P',''), 'pr'=c('',''), 'tr'=c('abcde','','',''), 'eq'="mu*RB5P"),
63+
'R5Pdilution'= list('su'=c('R5P',''), 'pr'=c('',''), 'tr'=c('abcde','','',''), 'eq'="mu*R5P"),
64+
'X5Pdilution'= list('su'=c('X5P',''), 'pr'=c('',''), 'tr'=c('abcde','','',''), 'eq'="mu*X5P"),
65+
'S7Pdilution'= list('su'=c('S7P',''), 'pr'=c('',''), 'tr'=c('abcdefg','','',''), 'eq'="mu*S7P"),
66+
'PYRdilution'= list('su'=c('PYR',''), 'pr'=c('',''), 'tr'=c('abc','','',''), 'eq'="mu*PYR"),
67+
'PGNdilution'= list('su'=c('PGN',''), 'pr'=c('',''), 'tr'=c('abcdef','','',''), 'eq'="mu*PGN"),
68+
'E4Pdilution'= list('su'=c('E4P',''), 'pr'=c('',''), 'tr'=c('abcd','','',''), 'eq'="mu*E4P"),
69+
'G1Pdilution'= list('su'=c('G1P',''), 'pr'=c('',''), 'tr'=c('abcdef','','',''), 'eq'="mu*G1P"))
70+
71+
# kinetic parameters
72+
kp=c('PTSrmaxPTS'=7829.78,
73+
'PTSKPTSa1'=3082.3,
74+
'PTSKPTSa2'=0.01,
75+
'PTSKPTSa3'=245.3,
76+
'PTSnPTSg6p'=3.66,
77+
'PTSKPTSg6p'=2.15,
78+
'PGIrmaxPGI'=650.988,
79+
'PGIKPGIeq'=0.1725,
80+
'PGIKPGIg6p'=2.9,
81+
'PGIKPGIf6p'=0.266,
82+
'PGIKPGIf6ppginh'=0.2,
83+
'PGIKPGIg6ppginh'=0.2,
84+
'PGMrmaxPGM'=0.839824,
85+
'PGMKPGMeq'=0.196,
86+
'PGMKPGMg6p'=1.038,
87+
'PGMKPGMg1p'=0.0136,
88+
'G6PDHrmaxG6PDH'=1.3802,
89+
'G6PDHKG6PDHg6p'=14.4,
90+
'G6PDHKG6PDHnadphg6pinh'=6.43,
91+
'G6PDHKG6PDHnadp'=0.0246,
92+
'G6PDHKG6PDHnadphnadpinh'=0.01,
93+
'cnadph'=0.062,
94+
'PFKrmaxPFK'=1840.58,
95+
'PFKKPFKatps'=0.123,
96+
'PFKKPFKadpc'=4.14,
97+
'PFKKPFKf6ps'=0.325,
98+
'PFKKPFKpep'=3.26,
99+
'PFKKPFKadpb'=3.89,
100+
'PFKKPFKampb'=3.2,
101+
'PFKKPFKadpa'=128,
102+
'PFKKPFKampa'=19.1,
103+
'PFKLPFK'=5629070,
104+
'PFKnPFK'=11.1,
105+
'cadp'=0.582,
106+
'camp'=0.954783,
107+
'TArmaxTA'=10.8716,
108+
'TAKTAeq'=1.05,
109+
'TK1rmaxTKa'=9.47338,
110+
'TK1KTKaeq'=1.2,
111+
'TK2rmaxTKb'=86.5586,
112+
'TK2KTKbeq'=10,
113+
'MURSYNv'=0.00043711,
114+
'ALDrmaxALDO'=17.4146,
115+
'ALDkALDOeq'=0.144,
116+
'ALDkALDOfdp'=1.75,
117+
'ALDkALDOgap'=0.088,
118+
'ALDVALDOblf'=2,
119+
'ALDkALDOdhap'=0.088,
120+
'ALDkALDOgapinh'=0.6,
121+
'GAPDHrmaxGAPDH'=921.594,
122+
'GAPDHKGAPDHeq'=0.63,
123+
'GAPDHKGAPDHgap'=0.683,
124+
'GAPDHKGAPDHpgp'=0.0000104,
125+
'GAPDHKGAPDHnad'=0.252,
126+
'GAPDHKGAPDHnadh'=1.09,
127+
'cnad'=1.4644,
128+
'cnadh'=0.0934,
129+
'TPIrmaxTIS'=68.6747,
130+
'TPIkTISeq'=1.39,
131+
'TPIkTISdhap'=2.8,
132+
'TPIkTISgap'=0.3,
133+
'TRPv'=0.001037,
134+
'GDHrmaxG3PDH'=0.0116204,
135+
'GDHKG3PDHdhap'=1,
136+
'PGKrmaxPGK'=3021.77,
137+
'PGKKPGKeq'=1934.4,
138+
'PGKKPGKadp'=0.185,
139+
'PGKKPGKatp'=0.653,
140+
'PGKKPGKpgp'=0.0468,
141+
'PGKKPGKpg3'=0.473,
142+
'SERSYNrmaxSerSynth'=0.0257121,
143+
'SERSYNKSerSynthpg3'=1,
144+
'PGMrmaxPGluMu'=89.0497,
145+
'PGMKPGluMueq'=0.188,
146+
'PGMKPGluMupg3'=0.2,
147+
'PGMKPGluMupg2'=0.369,
148+
'ENOrmaxENO'=330.448,
149+
'ENOKENOeq'=6.73,
150+
'ENOKENOpg2'=0.1,
151+
'ENOKENOpep'=0.135,
152+
'PYKrmaxPK'=0.0611315,
153+
'PYKKPKpep'=0.31,
154+
'PYKnPK'=4,
155+
'PYKLPK'=1000,
156+
'PYKKPKatp'=22.5,
157+
'PYKKPKfdp'=0.19,
158+
'PYKKPKamp'=0.2,
159+
'PYKKPKadp'=0.26,
160+
'PPCrmaxpepCxylase'=0.107021,
161+
'PPCKpepCxylasefdp'=0.7,
162+
'PPCnpepCxylasefdp'=4.21,
163+
'PPCKpepCxylasepep'=4.07,
164+
'SYN1rmaxSynth1'=0.019539,
165+
'SYN1KSynth1pep'=1,
166+
'SYN2rmaxSynth2'=0.0736186,
167+
'SYN2KSynth2pyr'=1,
168+
'DAHPSYNrmaxDAHPS'=0.107953,
169+
'DAHPSYNnDAHPSe4p'=2.6,
170+
'DAHPSYNnDAHPSpep'=2.2,
171+
'DAHPSYNKDAHPSe4p'=0.035,
172+
'DAHPSYNKDAHPSpep'=0.0053,
173+
'PDHrmaxPDH'=6.05953,
174+
'PDHnPDH'=3.68,
175+
'PDHKPDHpyr'=1159,
176+
'METSYNv'=0.0022627,
177+
'GNDrmaxPGDH'=16.2324,
178+
'GNDKPGDHpg'=37.5,
179+
'GNDKPGDHnadp'=0.0506,
180+
'GNDKPGDHnadphinh'=0.0138,
181+
'GNDKPGDHatpinh'=208,
182+
'catp'=4.27,
183+
'cnadp'=0.196759,
184+
'RPIrmaxR5PI'=4.83841,
185+
'RPIKR5PIeq'=4,
186+
'RPErmaxRu5P'=6.73903,
187+
'RPEKRu5Peq'=1.4,
188+
'RPPrmaxRPPK'=0.0129005,
189+
'RPPKRPPKrib5p'=0.1,
190+
'G1PATrmaxG1PAT'=0.00752546,
191+
'G1PATKG1PATfdp'=0.119,
192+
'G1PATnG1PATfdp'=1.2,
193+
'G1PATKG1PATatp'=4.42,
194+
'G1PATKG1PATg1p'=3.2,
195+
'mu'=0.0000278)
196+

0 commit comments

Comments
 (0)