Supplenentary text 2A
diff from Ec_iAF1260_flux2.xml {Feist, 2007 #381} to Ec_iAF1260_noisozyme.xml used for initial
FBA
*** Ec_iAF1260_flux2.xml 2007-04-05 12:25:02.000000000 +0900
--- Ec_iAF1260_noisozyme.xml 2009-04-07 22:46:02.000000000 +0900
***************
*** 30794,30801 ****
! GENE_ASSOCIATION: ( b2097 or b1773 or b2925 )
! PROTEIN_ASSOCIATION: ( FbaB ) or ( B1773 ) or ( FbaA )
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 4.1.2.13
--- 30794,30801 ----
! GENE_ASSOCIATION: b2925
! PROTEIN_ASSOCIATION: FbaA
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 4.1.2.13
***************
*** 30821,30828 ****
! GENE_ASSOCIATION: ( b3925 or b4232 )
! PROTEIN_ASSOCIATION: ( GlpX ) or ( Fbp )
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 3.1.3.11
--- 30821,30828 ----
! GENE_ASSOCIATION: b4232
! PROTEIN_ASSOCIATION: Fbp
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 3.1.3.11
***************
*** 55225,55232 ****
! GENE_ASSOCIATION: ( b3916 or b1723 )
! PROTEIN_ASSOCIATION: ( PfkA ) or ( PfkB )
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 2.7.1.11
--- 55225,55232 ----
! GENE_ASSOCIATION: b3916
! PROTEIN_ASSOCIATION: PfkA
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 2.7.1.11
***************
*** 55693,55700 ****
! GENE_ASSOCIATION: ( b3612 or b4395 or b0755 )
! PROTEIN_ASSOCIATION: ( YibO ) or ( GpmB ) or ( GpmA )
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 5.4.2.1
--- 55693,55700 ----
! GENE_ASSOCIATION: b0755
! PROTEIN_ASSOCIATION: GpmA
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 5.4.2.1
***************
*** 60705,60712 ****
! GENE_ASSOCIATION: ( b1854 or b1676 )
! PROTEIN_ASSOCIATION: ( Pyka ) or ( Pykf )
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 2.7.1.40
--- 60705,60712 ----
! GENE_ASSOCIATION: b1676
! PROTEIN_ASSOCIATION: Pykf
SUBSYSTEM: S_GlycolysisGluconeogenesis
PROTEIN_CLASS: 2.7.1.40
***************
*** 61808,61815 ****
! GENE_ASSOCIATION: ( b3386 or b4301 )
! PROTEIN_ASSOCIATION: ( Rpeec ) or ( SgcE )
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 5.1.3.1
--- 61808,61815 ----
! GENE_ASSOCIATION: b3386
! PROTEIN_ASSOCIATION: Rpeec
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 5.1.3.1
***************
*** 61834,61841 ****
! GENE_ASSOCIATION: ( b2914 or b4090 )
! PROTEIN_ASSOCIATION: ( RpiA ) or ( RpiB )
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 5.3.1.6
--- 61834,61841 ----
! GENE_ASSOCIATION: b2914
! PROTEIN_ASSOCIATION: RpiA
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 5.3.1.6
***************
*** 63643,63650 ****
! GENE_ASSOCIATION: ( b2464 or b0008 )
! PROTEIN_ASSOCIATION: ( TalA ) or ( TalB )
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.2
--- 63643,63650 ----
! GENE_ASSOCIATION: b0008
! PROTEIN_ASSOCIATION: TalB
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.2
***************
*** 64824,64831 ****
! GENE_ASSOCIATION: ( b2935 or b2465 )
! PROTEIN_ASSOCIATION: ( TktA ) or ( TktB )
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
--- 64824,64831 ----
! GENE_ASSOCIATION: b2935
! PROTEIN_ASSOCIATION: TktA
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
***************
*** 64852,64859 ****
! GENE_ASSOCIATION: ( b2935 or b2465 )
! PROTEIN_ASSOCIATION: ( TktA ) or ( TktB )
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
--- 64852,64859 ----
! GENE_ASSOCIATION: b2935
! PROTEIN_ASSOCIATION: TktA
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
Supplenentary text 2B
diff from Ec_iAF1260_noisozyme.xml to Ec_iAF1260_noisozyme_S17P.xml used for second
FBA considering result from double knockout
*** Ec_iAF1260_noisozyme.xml 2009-04-07 22:46:02.000000000 +0900
--- Ec_iAF1260_noisozyme_S17P.xml 2009-04-08 23:34:45.000000000 +0900
***************
*** 1437,1442 ****
--- 1437,1443 ----
+
***************
*** 55252,55257 ****
--- 55253,55316 ----
+
+
+ GENE_ASSOCIATION: b3916
+ PROTEIN_ASSOCIATION: PfkA
+ SUBSYSTEM: S_Pentose_Phosphate_Pathway
+ PROTEIN_CLASS: 2.7.1.11
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ GENE_ASSOCIATION: b2925
+ PROTEIN_ASSOCIATION: FbaA
+ SUBSYSTEM: S_Pentose_Phosphate_Pathway
+ PROTEIN_CLASS: 4.1.2.13
+
+
+
+
+
+
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+
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GENE_ASSOCIATION: b3916
***************
*** 64824,64831 ****
! GENE_ASSOCIATION: b2935
! PROTEIN_ASSOCIATION: TktA
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
--- 64883,64890 ----
! GENE_ASSOCIATION: ( b2935 or b2465 )
! PROTEIN_ASSOCIATION: ( TktA ) or ( TktB )
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
***************
*** 64852,64859 ****
! GENE_ASSOCIATION: b2935
! PROTEIN_ASSOCIATION: TktA
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
--- 64911,64918 ----
! GENE_ASSOCIATION: ( b2935 or b2465 )
! PROTEIN_ASSOCIATION: ( TktA ) or ( TktB )
SUBSYSTEM: S_Pentose_Phosphate_Pathway
PROTEIN_CLASS: 2.2.1.1
Supplenentary text 2C RunFBAmodel1.m
Script for initial FBA prediction using COBRA toolbox {Becker, 2007 #544}.
clc
% with alterarions concering discrepancy in single deletion
% model used
% without isozyme => 1
% with isozyme => 2
use_model = 1;
% method used
% linearMOMA => 1
% FBA => 2
use_method = 2;
% airation condition
% aerobic o2 > -18 => 1
% semi aerobic o2 > -5 => 2
% anaerobic => 3
% semi aerobic o2 > -8 => 4
% semi aerobic o2 > -12 => 5
% aerobic o2 > -8 => 6
% aerobic o2 > -12 => 7
air_cond = 1;
% read model
switch use_model
case 1
disp('Ec_iAF1260_flux noisozyme...');
model = readCbModel('../Ec_iAF1260_noisozyme');
case 2
disp('Ec_iAF1260_flux2...');
model = readCbModel('../Ec_iAF1260_flux2');
end
% air_cond
switch air_cond
case 1
disp('aerobic(o2 18)...');
model = changeRxnBounds(model,'EX_o2(e)' , -18, 'l');
case 2
disp('semi aerobic(o2 5)...');
model = changeRxnBounds(model,'EX_o2(e)' , -5, 'l');
model = changeRxnBounds(model, {'CADVtpp','DMSOR1','DMSOR2','FRD2','FRD3','HYD1pp','HYD2pp','HYD3pp',...
'NO2t2rpp','NTRIR2x','PFL','RNTR1c','RNTR2c','RNTR3c','RNTR4c','TMAOR1','TMAOR2'}, 100, 'u');
model = changeRxnBounds(model,'NO2t2rpp' , -100, 'l');
model = changeRxnBounds(model,'CYTBO3_4pp' , 0, 'b');
case 3
disp('anaerobic...');
model = changeRxnBounds(model,'EX_o2(e)' , 0, 'b');
model = changeRxnBounds(model, {'CADVtpp','DMSOR1','DMSOR2','FRD2','FRD3','HYD1pp','HYD2pp','HYD3pp',...
'NO2t2rpp','NTRIR2x','PFL','RNTR1c','RNTR2c','RNTR3c','RNTR4c','TMAOR1','TMAOR2'}, 100, 'u');
model = changeRxnBounds(model,'NO2t2rpp' , -100, 'l');
model = changeRxnBounds(model,'CYTBO3_4pp' , 0, 'b');
case 4
disp('semi aerobic(o2 8)...');
model = changeRxnBounds(model,'EX_o2(e)' , -8, 'l');
model = changeRxnBounds(model, {'CADVtpp','DMSOR1','DMSOR2','FRD2','FRD3','HYD1pp','HYD2pp','HYD3pp',...
'NO2t2rpp','NTRIR2x','PFL','RNTR1c','RNTR2c','RNTR3c','RNTR4c','TMAOR1','TMAOR2'}, 100, 'u');
model = changeRxnBounds(model,'NO2t2rpp' , -100, 'l');
model = changeRxnBounds(model,'CYTBO3_4pp' , 0, 'b');
case 5
disp('semi aerobic(o2 12)...');
model = changeRxnBounds(model,'EX_o2(e)' , -12, 'l');
model = changeRxnBounds(model, {'CADVtpp','DMSOR1','DMSOR2','FRD2','FRD3','HYD1pp','HYD2pp','HYD3pp',...
'NO2t2rpp','NTRIR2x','PFL','RNTR1c','RNTR2c','RNTR3c','RNTR4c','TMAOR1','TMAOR2'}, 100, 'u');
model = changeRxnBounds(model,'NO2t2rpp' , -100, 'l');
model = changeRxnBounds(model,'CYTBO3_4pp' , 0, 'b');
case 6
disp('aerobic(o2 8)...');
model = changeRxnBounds(model,'EX_o2(e)' , -8, 'l');
case 7
disp('aerobic(o2 12)...');
model = changeRxnBounds(model,'EX_o2(e)' , -12, 'l');
end
% output file
file = [ 'result_' num2str( use_model ) '_' num2str( air_cond ) '_' num2str( use_method ) '.txt' ];
fid = fopen( file,'w' );
% medium condition
% Casamino Acid
model = changeRxnBounds(model, {'EX_ala_L(e)','EX_arg_L(e)','EX_asp_L(e)','EX_cys_L(e)','EX_glu_L(e)',...
'EX_gly(e)','EX_his_L(e)','EX_ile_L(e)','EX_leu_L(e)','EX_lys_L(e)','EX_met_L(e)','EX_phe_L(e)','EX_pro_L(e)',...
'EX_ser_L(e)','EX_thr_L(e)','EX_trp_L(e)','EX_tyr_L(e)','EX_val_L(e)'},...
[-0.21 -0.08 -0.22 0.00 -0.62 -0.12 -0.07 -0.18 -0.22 -0.23 -0.05 -0.12 -0.41 -0.11 -0.08 0.00 -0.01 -0.28],'l');
% carbon source
CarbonSourceCond = {'noC','glc','mnl','fru','glyc','ac','succ','glu_L','glcur','glcn','xyl','mix'};
CarbonSourceName = {'EX_glc(e)','EX_mnl(e)','EX_fru(e)','EX_glyc(e)','EX_ac(e)',...
'EX_succ(e)','EX_glu_L(e)','EX_glcur(e)','EX_glcn(e)','EX_xyl_D(e)'};
CarbonSourceList = [0 0 0 0 0 0 0 0 0 0];
CarbonSourceList = [CarbonSourceList;-6 * eye(length(CarbonSourceList))];
CarbonSourceList = [CarbonSourceList;[0 0 0 -4 0 -4 0 0 0 0] ];
% additional glu_L(e)
for i = 1 : length(CarbonSourceList)
CarbonSourceList(i,7) = CarbonSourceList(i,7) + (-0.62);
end
% 2nd deletion list
RxnDeletionList = {'-----','PGI','G6PDH2r','ICL','PPC','ME1','TALA','PYK'};
% 1st deletion list
GeneDeletionList = {'-----','b0114','b0115','b2779','b2925','b2097','b4232','b1779','b2388','b0720',...
'b2029','b0755','b4395','b3612','b1136','b0116','b2463','b3403','b3916','b1723','b4025',...
'b2926','b3956','b1702','b1854','b1676','b3386','b2914','b4090','b1479','b2464','b0008',...
'b2935','b2465','b3919','b1852'};
% altlations to the model for mimic single gene deletion
% for tpiA
model = changeRxnBounds(model,'G3PD2' , -0.2, 'l'); %for TpiA; required for production of phospholipid but excess flux lead to growth of tpiA by exporting DHA via DHAP -> glyc3P -> glyc -> DHA
model = changeRxnBounds(model,'F6PA' , 0, 'b'); %for TpiA; presence of this reaction is not confirmed in vivo and contradictory for the phenotypes of many mutants, like pgi-zwf, fbaA, pfkAB,
model = changeRxnBounds(model,'EDD' , 0, 'b'); % for TpiA; known to be repressed except for gluconate and other carbon sources
model = changeRxnBounds(model,'GLCDpp' , 0, 'b'); % for tpiA; this eraction is not active without addition of cofacter PQQ
model = changeRxnBounds(model,'MGSA' , 0.25, 'u'); %for TpiA; known to operate in TpiA
model = changeRxnBounds(model,'DRPA' , 0.25, 'u'); % for TpiA; R5P to nucleotides and degradation
% for PDH; limit production of AcCoA
model = changeRxnBounds(model,'POX' , 0.1, 'u'); % for from pyruvate to acetate
model = changeRxnBounds(model,'ACALD' , 0.1, 'u'); % stop from acetoaldehyde
model = changeRxnBounds(model,'ALDD2x' , 0.1, 'u'); % stop from acetoaldehyde via acetate
model = changeRxnBounds(model,'CITL' , 0.1, 'u'); % stop from citrate via acetate
model = changeRxnBounds(model,'GLYAT' , -0.1, 'l'); % stop threonine to glycone
fprintf( fid, 'Gene1tGene2tSourcetmutnutYt');
for i = 1 : length(CarbonSourceName)
fprintf( fid, '%st', CarbonSourceName{i});
end
% additional flux shown
fprintf( fid, 'RPItEX_o2(e)tPGItTALAtRPEtTKT1tPFKtPSKtICLtZwft');
fprintf( fid, 'n');
for i = 1 : length(RxnDeletionList)
disp(RxnDeletionList{i})
if i == 1
modelx = model;
else
modelx = changeRxnBounds(model, RxnDeletionList{i}, 0, 'b');
% special alterations for 2ndary deletion
if findRxnIDs(model,RxnDeletionList{i}) == findRxnIDs(model,'PPC')
% PPC and PPCK
modelx = changeRxnBounds(modelx, 'PPCK', 0, 'b');
elseif findRxnIDs(model,RxnDeletionList{i}) == findRxnIDs(model,'ME1')
% ME1 and ME2
modelx = changeRxnBounds(modelx, 'ME2', 0, 'b');
end
end
for j = 1 : length(GeneDeletionList)
disp(GeneDeletionList{j})
modelxx = modelx ;
for k = 1 : length(CarbonSourceList)
modelxxx = changeRxnBounds(modelxx,{'EX_glc(e)','EX_mnl(e)','EX_fru(e)','EX_glyc(e)','EX_ac(e)','EX_succ(e)',...
'EX_glu_L(e)','EX_glcur(e)','EX_glcn(e)','EX_xyl_D(e)'}, CarbonSourceList(k,:), 'l');
modelxxw = changeRxnBounds(model,{'EX_glc(e)','EX_mnl(e)','EX_fru(e)','EX_glyc(e)','EX_ac(e)','EX_succ(e)',...
'EX_glu_L(e)','EX_glcur(e)','EX_glcn(e)','EX_xyl_D(e)'}, CarbonSourceList(k,:), 'l');
% alterations in specific carbon source
% {'noC','glc','mnl','fru','glyc','ac','succ','glu_L','glcur','glcn','xyl','mix'};
if k == 1 % Casamino acid only
modelxxx = changeRxnBounds(modelxxx, { 'ICL', 'MALS' }, 100, 'u');
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, { 'ICL', 'MALS' }, 100, 'u');
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 2 % glucose
%glucose
modelxxx = changeRxnBounds(modelxxx, 'PGI', -0.1, 'l'); %; limit reverseflux of PGI (thermodynamical constraint considering intracellular conc)
modelxxw = changeRxnBounds(modelxxw, 'PGI', -0.1, 'l');
elseif k == 3 % mannitol
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u'); %limit reverseflux of TKT2 (thermodynamical constraint considering intracellular conc)
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 4 % flucose
%frucose
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u');; %limit reverseflux of TKT2 (thermodynamical constraint considering intracellular conc)
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 5 % glycerol
modelxxx = changeRxnBounds(modelxxx, { 'G3PD5', 'G3PD6', 'G3PD7', 'GLYK' }, 100, 'u');
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, { 'G3PD5', 'G3PD6', 'G3PD7', 'GLYK' }, 100, 'u');
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 6 % acetate
modelxxx = changeRxnBounds(modelxxx, 'ACS', 100, 'u');
modelxxx = changeRxnBounds(modelxxx, { 'ICL', 'MALS' }, 100, 'u');
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, { 'ICL', 'MALS' }, 100, 'u');
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, 'ACS', 100, 'u');
elseif k == 7 % succinate
modelxxx = changeRxnBounds(modelxxx, { 'ICL', 'MALS' }, 100, 'u');
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, { 'ICL', 'MALS' }, 100, 'u');
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 8 % glutamate
modelxxx = changeRxnBounds(modelxxx, { 'ICL', 'MALS' }, 100, 'u');
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, { 'ICL', 'MALS' }, 100, 'u');
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 9 % glucronate
modelxxx = changeRxnBounds(modelxxx,'G6PDH2r' , 1, 'u');
modelxxw = changeRxnBounds(modelxxw,'G6PDH2r' , 1, 'u');
elseif k == 10 % gluconate
modelxxx = changeRxnBounds(modelxxx,'EDD' , 100, 'u');
modelxxw = changeRxnBounds(modelxxw,'EDD' , 100, 'u');
modelxxx = changeRxnBounds(modelxxx,'G6PDH2r' , 1, 'u');
modelxxw = changeRxnBounds(modelxxw,'G6PDH2r' , 1, 'u');
elseif k == 11 % xylose
modelxxx = changeRxnBounds(modelxxx, 'RPE', 0.1, 'u');
modelxxx = changeRxnBounds(modelxxx, 'TKT1', -0.1, 'l');
modelxxx = changeRxnBounds(modelxxx, 'TKT2', -0.1, 'l');
modelxxx = changeRxnBounds(modelxxx, { 'XYLI1', 'XYLK' , 'XYLabcpp' } , 100, 'u');
modelxxw = changeRxnBounds(modelxxw, 'RPE', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, 'TKT1', -0.1, 'l');
modelxxw = changeRxnBounds(modelxxw, 'TKT2', -0.1, 'l');
modelxxw = changeRxnBounds(modelxxw, { 'XYLI1', 'XYLK' , 'XYLabcpp' } , 100, 'u');
elseif k == 12 % glycerol+Succinate
modelxxx = changeRxnBounds(modelxxx, { 'G3PD5', 'G3PD6', 'G3PD7', 'GLYK' }, 100, 'u');
modelxxx = changeRxnBounds(modelxxx, { 'ICL', 'MALS' }, 100, 'u');
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u');
modelxxw = changeRxnBounds(modelxxw, { 'G3PD5', 'G3PD6', 'G3PD7', 'GLYK' }, 100, 'u');
modelxxw = changeRxnBounds(modelxxw, { 'ICL', 'MALS' }, 100, 'u');
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
end
if i == 1 % reconfirm 2nd deletion
modelxxx = modelxxx;
else
modelxxx = changeRxnBounds(modelxxx, RxnDeletionList{i}, 0, 'b');
end
if GeneDeletionList{j} == '-----'
modelxxx = modelxxx;
else
modelxxx = deleteModelGenes(modelxxx, GeneDeletionList{j});
end
switch use_method
case 1
solutionDel = linearMOMA(modelxxw,modelxxx,'max');
case 2
solutionDel = optimizeCbModel(modelxxx,'max',true,false);
end
mu = solutionDel.f; %mu
fprintf( fid, '%st', RxnDeletionList{i});
fprintf( fid, '%st', GeneDeletionList{j});
fprintf( fid, '%st', CarbonSourceCond{k});
fprintf( fid, '%7.3ft', mu);
if k == 1 | k == 12
fprintf( fid, '%7.3ft%7.3ft', 0, 0 );
else
if length(solutionDel.x) == 0;
fprintf( fid, 'nosolt');
else
uptakeFlux = solutionDel.x(findRxnIDs(model,CarbonSourceName{k-1}));
Y = mu/(-1 * uptakeFlux);
fprintf( fid, '%7.3ft', uptakeFlux);
fprintf( fid, '%7.3ft', Y);
end
end
if length(solutionDel.x) == 0;
fprintf( fid, 'nosolt');
else
for l = 1 : length(CarbonSourceName)
uptakeFlux = solutionDel.x(findRxnIDs(model,CarbonSourceName{l}));
fprintf( fid, '%7.3ft', uptakeFlux);
end
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'RPI')));
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'EX_o2(e)')));
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'PGI')));
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'TALA')));
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'RPE')));
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'TKT1')));
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'PFK')));
%fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'PSK')));
fprintf( fid, '%7.3ft', '-');
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'ICL')));
fprintf( fid, '%7.3ft', solutionDel.x(findRxnIDs(modelxxx,'G6PDH2r')));
end
modelxxw = model;
modelxxx = modelxx;
fprintf( fid, 'n');
end
fprintf( fid, 'n');
modelxx = modelx;
end
modelx = model;
fprintf( fid, 'n');
end
Supplenentary text 2D diff from RunFBAmodel1.m to RunFBAmodel2.m
Diference of Script for initial FBA and second FBA
*** RunFBAmodel1.m 2009-05-01 19:23:14.000000000 +0900
--- RunFBAmodel2.m 2009-05-01 19:26:44.000000000 +0900
***************
*** 1,9 ****
clc
! % with alterarions concering discrepancy in single deletion
% model used
% without isozyme => 1
% with isozyme => 2
! use_model = 1;
% method used
% linearMOMA => 1
--- 1,11 ----
clc
! % with alterarions concering discrepancy in double deletion
!
% model used
% without isozyme => 1
% with isozyme => 2
! % without isozyme,S17P => 3
! use_model = 3;
% method used
% linearMOMA => 1
***************
*** 28,36 ****
--- 30,42 ----
case 2
disp('Ec_iAF1260_flux2...');
model = readCbModel('../Ec_iAF1260_flux2');
+ case 3
+ disp('Ec_iAF1260_noisozyme_S17P...');
+ model = readCbModel('../Ec_iAF1260_noisozyme_S17P');
end
+
% air_cond
switch air_cond
case 1
***************
*** 70,76 ****
case 7
disp('aerobic(o2 12)...');
model = changeRxnBounds(model,'EX_o2(e)' , -12, 'l');
-
end
% output file
--- 76,81 ----
***************
*** 79,85 ****
% medium condition
! % Casamino Acid
model = changeRxnBounds(model, {'EX_ala_L(e)','EX_arg_L(e)','EX_asp_L(e)','EX_cys_L(e)','EX_glu_L(e)',...
'EX_gly(e)','EX_his_L(e)','EX_ile_L(e)','EX_leu_L(e)','EX_lys_L(e)','EX_met_L(e)','EX_phe_L(e)','EX_pro_L(e)',...
'EX_ser_L(e)','EX_thr_L(e)','EX_trp_L(e)','EX_tyr_L(e)','EX_val_L(e)'},...
--- 84,90 ----
% medium condition
! % Casamino Acid
model = changeRxnBounds(model, {'EX_ala_L(e)','EX_arg_L(e)','EX_asp_L(e)','EX_cys_L(e)','EX_glu_L(e)',...
'EX_gly(e)','EX_his_L(e)','EX_ile_L(e)','EX_leu_L(e)','EX_lys_L(e)','EX_met_L(e)','EX_phe_L(e)','EX_pro_L(e)',...
'EX_ser_L(e)','EX_thr_L(e)','EX_trp_L(e)','EX_tyr_L(e)','EX_val_L(e)'},...
***************
*** 99,142 ****
end
% 2nd deletion list
RxnDeletionList = {'-----','PGI','G6PDH2r','ICL','PPC','ME1','TALA','PYK'};
% 1st deletion list
GeneDeletionList = {'-----','b0114','b0115','b2779','b2925','b2097','b4232','b1779','b2388','b0720',...
'b2029','b0755','b4395','b3612','b1136','b0116','b2463','b3403','b3916','b1723','b4025',...
'b2926','b3956','b1702','b1854','b1676','b3386','b2914','b4090','b1479','b2464','b0008',...
'b2935','b2465','b3919','b1852'};
! % altlations to the model for mimic single gene deletion
!
! % for tpiA
! model = changeRxnBounds(model,'G3PD2' , -0.2, 'l'); %for TpiA; required for production of phospholipid but excess flux lead to growth of tpiA by exporting DHA via DHAP -> glyc3P -> glyc -> DHA
! model = changeRxnBounds(model,'F6PA' , 0, 'b'); %for TpiA; presence of this reaction is not confirmed in vivo and contradictory for the phenotypes of many mutants, like pgi-zwf, fbaA, pfkAB,
! model = changeRxnBounds(model,'EDD' , 0, 'b'); % for TpiA; known to be repressed except for gluconate and other carbon sources
! model = changeRxnBounds(model,'GLCDpp' , 0, 'b'); % for tpiA; this eraction is not active without addition of cofacter PQQ
! model = changeRxnBounds(model,'MGSA' , 0.25, 'u'); %for TpiA; known to operate in TpiA
! model = changeRxnBounds(model,'DRPA' , 0.25, 'u'); % for TpiA; R5P to nucleotides and degradation
! % for PDH; limit production of AcCoA
model = changeRxnBounds(model,'POX' , 0.1, 'u'); % for from pyruvate to acetate
model = changeRxnBounds(model,'ACALD' , 0.1, 'u'); % stop from acetoaldehyde
model = changeRxnBounds(model,'ALDD2x' , 0.1, 'u'); % stop from acetoaldehyde via acetate
model = changeRxnBounds(model,'CITL' , 0.1, 'u'); % stop from citrate via acetate
model = changeRxnBounds(model,'GLYAT' , -0.1, 'l'); % stop threonine to glycone
!
fprintf( fid, 'Gene1\tGene2\tSource\tmu\tnu\tY\t');
for i = 1 : length(CarbonSourceName)
fprintf( fid, '%s\t', CarbonSourceName{i});
end
! % additional flux shown
fprintf( fid, 'RPI\tEX_o2(e)\tPGI\tTALA\tRPE\tTKT1\tPFK\tPSK\tICL\tZwf\t');
-
fprintf( fid, '\n');
for i = 1 : length(RxnDeletionList)
--- 104,159 ----
end
% 2nd deletion list
+ %RxnDeletionList = {'ICL'};
RxnDeletionList = {'-----','PGI','G6PDH2r','ICL','PPC','ME1','TALA','PYK'};
% 1st deletion list
GeneDeletionList = {'-----','b0114','b0115','b2779','b2925','b2097','b4232','b1779','b2388','b0720',...
'b2029','b0755','b4395','b3612','b1136','b0116','b2463','b3403','b3916','b1723','b4025',...
'b2926','b3956','b1702','b1854','b1676','b3386','b2914','b4090','b1479','b2464','b0008',...
'b2935','b2465','b3919','b1852'};
+ %GeneDeletionList = {'-----','b4232','b3919','b0115'};
+ %GeneDeletionList = {'-----'};
+ % altlations to the model
+ % for TpiA
+ model = changeRxnBounds(model,'G3PD2' , -0.2, 'l'); %for TpiA
+ model = changeRxnBounds(model,'F6PA' , 0, 'b'); %for TpiA, pgi-zwf
+ model = changeRxnBounds(model,'EDD' , 0, 'b'); % except for gluconate
+ model = changeRxnBounds(model,'GLCDpp' , 0, 'b'); % to glcn 5dglcd and export
! model = changeRxnBounds(model,'MGSA' , 0, 'b'); % Activate only on TpiA mutant
! model = changeRxnBounds(model,'DRPA' , 0, 'b'); % for TpiA
! % for PDH
model = changeRxnBounds(model,'POX' , 0.1, 'u'); % for from pyruvate to acetate
model = changeRxnBounds(model,'ACALD' , 0.1, 'u'); % stop from acetoaldehyde
model = changeRxnBounds(model,'ALDD2x' , 0.1, 'u'); % stop from acetoaldehyde via acetate
model = changeRxnBounds(model,'CITL' , 0.1, 'u'); % stop from citrate via acetate
model = changeRxnBounds(model,'GLYAT' , -0.1, 'l'); % stop threonine to glycone
! % for PckA-ME; stop TCA cycle to glycolysis
! model = changeRxnBounds(model,'THRD', 0, 'b'); % Thr to methylglyoxal
! model = changeRxnBounds(model,'THRAi', 0, 'b'); % Thr to methylglyoxal via gly
! model = changeRxnBounds(model,'GLXCL', 0, 'b'); % glyoxylate to 3PG
! model = changeRxnBounds(model,'OAADC', 0, 'b'); % oaa -> pyruvate + CO2
! model = changeRxnBounds(model,'MCITS', 0, 'b'); % oaa to pyruvate by 2-methylisocitrate cycle
!
! % for rpiA; block exit from ru5p -> ara5p -> lipidA etc -> export
! model = changeRxnBounds(model, 'EX_kdo2lipid4(e)', 0, 'b');
! model = changeRxnBounds(model, 'EX_lipa_cold(e)', 0, 'b');
! model = changeRxnBounds(model, 'EX_lipa(e)', 0, 'b');
! model = changeRxnBounds(model, 'EX_enlipa(e)', 0, 'b');
fprintf( fid, 'Gene1\tGene2\tSource\tmu\tnu\tY\t');
for i = 1 : length(CarbonSourceName)
fprintf( fid, '%s\t', CarbonSourceName{i});
end
! % additional flux 0401
fprintf( fid, 'RPI\tEX_o2(e)\tPGI\tTALA\tRPE\tTKT1\tPFK\tPSK\tICL\tZwf\t');
fprintf( fid, '\n');
for i = 1 : length(RxnDeletionList)
***************
*** 146,151 ****
--- 163,169 ----
modelx = model;
else
modelx = changeRxnBounds(model, RxnDeletionList{i}, 0, 'b');
+
% special alterations for 2ndary deletion
if findRxnIDs(model,RxnDeletionList{i}) == findRxnIDs(model,'PPC')
% PPC and PPCK
***************
*** 153,158 ****
--- 171,179 ----
elseif findRxnIDs(model,RxnDeletionList{i}) == findRxnIDs(model,'ME1')
% ME1 and ME2
modelx = changeRxnBounds(modelx, 'ME2', 0, 'b');
+ elseif findRxnIDs(model,RxnDeletionList{i}) == findRxnIDs(model,'TALA')
+ % Activate PSK on TALA deletion
+ modelx = changeRxnBounds(modelx, 'PSK', 100, 'u');
end
end
***************
*** 160,166 ****
disp(GeneDeletionList{j})
modelxx = modelx ;
!
for k = 1 : length(CarbonSourceList)
modelxxx = changeRxnBounds(modelxx,{'EX_glc(e)','EX_mnl(e)','EX_fru(e)','EX_glyc(e)','EX_ac(e)','EX_succ(e)',...
'EX_glu_L(e)','EX_glcur(e)','EX_glcn(e)','EX_xyl_D(e)'}, CarbonSourceList(k,:), 'l');
--- 181,187 ----
disp(GeneDeletionList{j})
modelxx = modelx ;
!
for k = 1 : length(CarbonSourceList)
modelxxx = changeRxnBounds(modelxx,{'EX_glc(e)','EX_mnl(e)','EX_fru(e)','EX_glyc(e)','EX_ac(e)','EX_succ(e)',...
'EX_glu_L(e)','EX_glcur(e)','EX_glcn(e)','EX_xyl_D(e)'}, CarbonSourceList(k,:), 'l');
***************
*** 179,185 ****
%glucose
modelxxx = changeRxnBounds(modelxxx, 'PGI', -0.1, 'l'); %; limit reverseflux of PGI (thermodynamical constraint considering intracellular conc)
modelxxw = changeRxnBounds(modelxxw, 'PGI', -0.1, 'l');
! elseif k == 3 % mannitol
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u'); %limit reverseflux of TKT2 (thermodynamical constraint considering intracellular conc)
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 4 % flucose
--- 200,207 ----
%glucose
modelxxx = changeRxnBounds(modelxxx, 'PGI', -0.1, 'l'); %; limit reverseflux of PGI (thermodynamical constraint considering intracellular conc)
modelxxw = changeRxnBounds(modelxxw, 'PGI', -0.1, 'l');
! elseif k == 3
! % mannitol
modelxxx = changeRxnBounds(modelxxx, 'TKT2', 0.1, 'u'); %limit reverseflux of TKT2 (thermodynamical constraint considering intracellular conc)
modelxxw = changeRxnBounds(modelxxw, 'TKT2', 0.1, 'u');
elseif k == 4 % flucose
***************
*** 239,250 ****
else
modelxxx = changeRxnBounds(modelxxx, RxnDeletionList{i}, 0, 'b');
end
!
! if GeneDeletionList{j} == '-----'
! modelxxx = modelxxx;
! else
! modelxxx = deleteModelGenes(modelxxx, GeneDeletionList{j});
! end
switch use_method
case 1
--- 261,282 ----
else
modelxxx = changeRxnBounds(modelxxx, RxnDeletionList{i}, 0, 'b');
end
!
! if GeneDeletionList{j} == '-----'
! modelxxx = modelxxx;
!
! elseif GeneDeletionList{j} == 'b2029' % gnd
! modelxxx = deleteModelGenes(modelxxx, GeneDeletionList{j});
! modelxxx = changeRxnBounds(modelxxx, 'EDD', 100, 'u');
! elseif GeneDeletionList{j} == 'b0008' % talB
! modelxxx = deleteModelGenes(modelxxx, GeneDeletionList{j});
! modelxxx = changeRxnBounds(modelxxx, 'PSK', 100, 'u');
! elseif GeneDeletionList{j} == 'b3919' % tpiA
! modelxxx = deleteModelGenes(modelxxx, GeneDeletionList{j});
! modelxxx = changeRxnBounds(modelxxx,'MGSA' , 0.5, 'u'); % Activate only on TpiA mutant
! else
! modelxxx = deleteModelGenes(modelxxx, GeneDeletionList{j});
! end
switch use_method
case 1
***************
*** 290,297 ****
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'RPE')));
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'TKT1')));
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'PFK')));
! %fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'PSK')));
! fprintf( fid, '%7.3f\t', '-');
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'ICL')));
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'G6PDH2r')));
end
--- 322,328 ----
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'RPE')));
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'TKT1')));
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'PFK')));
! fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'PSK')));
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'ICL')));
fprintf( fid, '%7.3f\t', solutionDel.x(findRxnIDs(modelxxx,'G6PDH2r')));
end