C-CoMP-STC / GEM-mit1002

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Growth on no carbon #54

Closed hgscott closed 5 months ago

hgscott commented 9 months ago

In #45 I got growth on my media with no carbon source.

hgscott commented 9 months ago

I used my test_growth_w_0_C test, and got the fluxes for all reactions with a non-zero flux in the solution.

ID Flux
rxn00836_c0 -0.002770596745527444
rxn00423_c0 0.023057242746862952
rxn00364_c0 0.16006877570670683
rxn03408_c0 0.009257971529604133
rxn04070_c0 0.00046176612425031686
rxn00199_c0 0.351224015432561
rxn01219_c0 -1.181103947621427e-14
rxn00800_c0 0.05837011106852836
rxn01705_c0 -0.0018140527307267318
rxn00179_c0 0.06963954833281986
rxn01218_c0 1.1811105595509738e-14
rxn02320_c0 -0.02207843116066436
rxn02504_c0 0.001385298372763764
rxn00898_c0 0.2035985688582041
rxn05334_c0 0.10355537532764489
rxn05040_c0 0.0018470644970097509
rxn02988_c0 -0.0009235322485021676
rxn01117_c0 -0.018515943059208263
rxn01331_c0 0.0004617661242503167
rxn00710_c0 0.04957297726805517
rxn02305_c0 0.000461766124250317
rxn03181_c0 0.009257971529604135
rxn02331_c0 -0.018515943059208267
rxn00337_c0 0.12528703252584075
rxn05346_c0 0.10355537532764485
rxn00416_c0 0.05594029468235762
rxn02376_c0 0.0961533889220579
rxn12512_c0 0.0009235322485093308
rxn00902_c0 -0.10456245768786578
rxn06672_c0 0.7266053157955137
rxn00649_c0 0.023057242746862952
rxn01739_c0 0.09303452107382608
rxn01974_c0 0.08876513093401922
rxn08971_c0 24.304198230714913
rxn00060_c0 0.0009235322485048363
rxn00225_c0 17.670086948325526
rxn05350_c0 0.10355537532764486
rxn05064_c0 8.430885443645283e-19
rxn00148_c0 -11.787395880004892
rxn00100_c0 0.0009235322485050847
rxn00789_c0 -0.02207843116066436
rxn03436_c0 0.06735161865303811
rxn00781_c0 -0.6508127494452326
rxn02264_c0 0.0009235322485048363
rxn09202_c0 0.007158189709953029
rxn00097_c0 0.44907140639956766
rxn05514_c0 -0.0004617661242515749
rxn02212_c0 0.09303452107382608
rxn05324_c0 -0.1035553753276449
rxn10481_c0 0.0004617661242503138
rxn00692_c0 -0.21144617552964204
rxn00802_c0 0.06963954833281986
rxn02160_c0 0.022078431160664356
rxn03958_c0 -0.11292007380768643
rxn01362_c0 -0.04957297726805517
rxn05329_c0 0.10355537532764485
rxn03174_c0 -0.0013852983727637646
rxn00549_c0 0.18834156496933918
rxn00727_c0 0.013147829792305768
rxn01354_c0 -0.0013522866064764136
rxn01445_c0 0.0004617661242503182
rxn08766_c0 0.10355537532764485
rxn02159_c0 0.022078431160664356
rxn05466_c0 2.3066699767773606
rxn00917_c0 0.039685981240750054
rxn00300_c0 0.0009235322485048751
rxn08792_c0 9.747754306539358
rxn05335_c0 0.057265517679624234
rxn03419_c0 0.0013852983727637642
rxn00272_c0 0.13823879242606715
rxn05595_c0 0.0009235322485031498
rxn05348_c0 0.10355537532764489
rxn11946_c0 0.0004617661242546346
rxn00907_c0 0.1694160922130541
rxn05458_c0 0.057265517679624234
rxn02404_c0 0.018515943059208267
rxn08822_c0 -0.028632758839812117
rxn05030_c0 0.009257971529604132
rxn05345_c0 0.09429740379804077
rxn00336_c0 13.640755776241132
rxn01465_c0 -0.04957297726805518
rxn01872_c0 -0.0961533889220579
rxn01301_c0 -0.03606013546756996
rxn01643_c0 -0.12528703252584075
rxn00248_c0 27.43463991316315
rxn00499_c0 -9.747754306539262
rxn00707_c0 0.0018140527307267315
rxn01269_c0 0.03407555738571135
rxn00392_c0 0.0004617661242546062
rxn00747_c0 0.23937242518751256
rxn00029_c0 0.0036941289940193448
rxn06673_c0 0.7266053157955137
rxn09128_c0 -0.02863275883981212
rxn05256_c0 0.05911737821442983
rxn02175_c0 0.0009235322485050846
rxn02835_c0 0.022078431160664356
rxn02774_c0 0.000461766124251575
rxn00555_c0 0.03703188611841653
rxn03435_c0 -0.06735161865303811
rxn03080_c0 0.0018470644970097507
rxn00849_c0 0.009257971529604135
rxn00737_c0 0.06735161865303811
rxn01256_c0 0.07711609453599538
rxn00777_c0 -0.1309466712947046
rxn01740_c0 -0.09303452107382608
rxn05327_c0 -0.10355537532764489
rxn00251_c0 12.952855734029388
rxn00790_c0 -0.07366883052734588
rxn03910_c0 0.11292007380768641
rxn00237_c0 0.09670380570280328
rxn00422_c0 -0.007158189709953032
rxn08311_c0 0.02863275883981212
rxn03175_c0 0.022078431160664356
rxn03421_c0 0.0013852983727637642
rxn05336_c0 -0.05726551767962424
rxn09210_c0 0.00715818970995303
rxn00182_c0 -20.354450227685195
rxn01045_c0 -0.3992784020935801
rxn00126_c0 0.0032323628697700675
rxn01015_c0 -0.007158189709953032
rxn05340_c0 -0.1035553753276449
rxn00405_c0 0.000923532248504836
rxn00904_c0 0.301165823171751
rxn03159_c0 0.009257971529604133
rxn01000_c0 0.04304053715028404
rxn01281_c0 0.007158189709953032
rxn00786_c0 -0.18834156496933918
rxn03908_c0 0.11292007380768644
rxn01100_c0 0.6508127494452326
rxn00838_c0 0.05837011106852836
rxn00102_c0 -0.9190249057994843
rxn01352_c0 -0.00046176612425031816
rxn01255_c0 0.09303452107382608
rxn05296_c0 0.15704457250847828
rxn01211_c0 0.09574726168570818
rxn00527_c0 -0.03407555738571136
rxn05322_c0 -0.10355537532764485
rxn00966_c0 -0.00046176612425196913
rxn01509_c0 -0.00046176612425031816
rxn02011_c0 0.009257971529604133
rxn00173_c0 -17.670086948325526
rxn08528_c0 0.0009235322485004913
rxn01145_c0 1.181620209884023e-14
rxn09176_c0 -0.8381695967628217
rxn01669_c0 -0.0009235322485020195
rxn08352_c0 0.010643269902359252
rxn09106_c0 0.021474569129859088
rxn00772_c0 0.0027705967455274446
rxn05338_c0 -0.10355537532764489
rxn03135_c0 -0.02207843116066436
rxn05337_c0 -0.10355537532764485
rxn03147_c0 0.07320706440309555
rxn03843_c0 0.009257971529604132
rxn01116_c0 -0.15130967885092267
rxn02811_c0 -0.10456245768786579
rxn03062_c0 0.10456245768786578
rxn00863_c0 0.022078431160664356
rxn09113_c0 0.021474569129859088
rxn02402_c0 -0.0009235322485019789
rxn05465_c0 0.6693397981158894
rxn01303_c0 0.03606013546756997
rxn00137_c0 0.00046176612425465443
rxn06023_c0 0.00046176612425157486
rxn00611_c0 -0.05010732796967121
rxn02286_c0 0.009257971529604133
rxn00832_c0 -0.09528549556375993
rxn01106_c0 0.9484505579508284
rxn00931_c0 -0.05135095786806216
rxn00066_c0 0.002770596745516178
rxn05115_c0 0.07320706440309555
rxn01573_c0 -0.06735161865303811
rxn00650_c0 -0.000461766124254652
rxn03167_c0 0.0013852983727637644
rxn00515_c0 0.0018140527307267315
rxn03005_c0 -0.0736688305273459
rxn03437_c0 0.06735161865303811
rxn04139_c0 0.00046176612425462385
rxn06723_c0 -0.01851594305920827
rxn00313_c0 0.07950715940441506
rxn00804_c0 -0.10456245768786579
rxn05325_c0 -0.10355537532764487
rxn02895_c0 0.0736688305273459
rxn00189_c0 18.567212253859708
rxn02508_c0 0.013147829792305764
rxn00420_c0 0.2976378085055958
rxn14334_c0 0.009257971529604132
rxn05005_c0 0.0004617661242502693
rxn02939_c0 0.0004617661242503167
rxn00048_c0 0.000923532248504875
rxn00853_c0 0.0009235322485018442
rxn05231_c0 0.0018140527307385483
rxn00283_c0 0.027773914588812402
rxn00379_c0 0.059117378214432914
rxn05330_c0 0.10355537532764485
rxn02475_c0 0.000923532248504875
rxn05339_c0 -0.10355537532764485
rxn03108_c0 0.000461766124250317
rxn01018_c0 0.049572977268055186
rxn03146_c0 0.01851594305920827
rxn03893_c0 0.0004617661242546276
rxn02789_c0 0.10456245768786578
rxn00410_c0 0.023902933406983674
rxn01333_c0 -0.028906695826423134
rxn12510_c0 0.0009235322485093309
rxn05342_c0 -0.09429740379804077
rxn00414_c0 0.11921252560087504
rxn00799_c0 -13.930737630975322
rxn02405_c0 0.018515943059208267
rxn00011_c0 -0.20359856885820407
rxn02200_c0 0.001385298372763764
rxn00791_c0 -0.013147829792305766
rxn00105_c0 0.0009235322484989685
rxn05029_c0 0.00046176612425026926
rxn02285_c0 -0.009257971529604132
rxn02303_c0 0.00046176612425458314
rxn05315_c0 -0.0004617661242515749
rxn05294_c0 0.0035112669545299237
rxn03907_c0 0.11292007380768644
rxn02834_c0 0.022078431160664356
rxn00459_c0 -0.9484505579508283
rxn00770_c0 0.16262396386665517
rxn14040_c0 0.009257971529604132
rxn05209_c0 -0.5722605517495352
rxn05618_c0 0.0004617661242515749
rxn00260_c0 -0.48980438746006644
rxn00461_c0 0.009257971529604135
rxn03136_c0 0.07320706440309556
rxn01387_c0 0.351224015432561
rxn02937_c0 0.07366883052734587
rxn00350_c0 -0.00046176612425458135
rxn03137_c0 0.09528549556375993
rxn00952_c0 0.03606013546756997
rxn01517_c0 -0.0018140527307385526
rxn00371_c0 0.005079427366779023
rxn05006_c0 0.00046176612425157497
rxn09234_c0 0.0018140527307385545
rxn01299_c0 0.002770596745527444
rxn05331_c0 0.10355537532764489
rxn02476_c0 0.09303452107382608
rxn01512_c0 0.0018140527307267318
rxn03841_c0 0.001385298372763764
rxn04954_c0 -0.03929249833734005
rxn06865_c0 -0.009257971529604133
rxn04113_c0 0.10227680390532716
rxn01257_c0 0.0013852983727637642
rxn09272_c0 13.730444439423652
rxn00943_c0 0.05726551767962423
rxn02213_c0 0.09303452107382608
rxn01127_c0 -1.181656931606497e-14
rxn05341_c0 -0.10355537532764487
rxn03393_c0 0.00046176612425462754
rxn00834_c0 0.039685981240750054
rxn05313_c0 0.19075351725153805
rxn01332_c0 0.09303452107382607
rxn00785_c0 0.12240298302449952
rxn00693_c0 0.03883073221308847
rxn03909_c0 0.11384360605618705
rxn01101_c0 0.29763780850559585
rxn03084_c0 0.07366883052734588
rxn03439_c0 0.009257971529604132
rxn05328_c0 -0.05726551767962424
rxn05323_c0 -0.057265517679624234
rxn01507_c0 1.1816569316064972e-14
rxn01790_c0 -0.0009235322485093308
rxn05651_c0 0.05957914433868449
rxn00077_c0 0.0004617661242474199
rxn01388_c0 -13.991979791673693
rxn03638_c0 0.03703188611841653
rxn02056_c0 -0.00046176612425157497
rxn01068_c0 -0.12614474432806574
rxn00851_c0 0.009257971529604133
rxn00141_c0 0.0027705967455274446
rxn01200_c0 0.028906695826423134
rxn01241_c0 0.09615338892205788
rxn05332_c0 0.05726551767962424
rxn00438_c0 0.00046176612425031377
rxn00763_c0 0.007158189709953029
rxn02473_c0 0.02207843116066436
rxn01434_c0 0.06963954833281986
rxn00912_c0 0.0009235322485093306
rxn09069_c0 -0.0036281054614534696
rxn00122_c0 0.00046176612425026915
rxn06076_c0 -0.0018140527307385424
rxn05344_c0 0.057265517679624234
rxn01521_c0 -1.1811525038933707e-14
rxn03394_c0 0.00046176612425462385
rxn00338_c0 0.0009235322485021676
rxn02373_c0 -0.06963954833281985
rxn00085_c0 19.064057937899648
rxn00119_c0 0.06808892032726342
rxn01466_c0 0.01064326990235925
rxn00974_c0 13.99197979167369
rxn02008_c0 0.009257971529604133
rxn03904_c0 0.009257971529604133
rxn02288_c0 0.0004617661242545831
rxn10199_c0 0.009257971529604132
rxn00409_c0 0.1582547229759683
rxn05295_c0 0.05517001038817757
rxn00840_c0 -0.0018140527307267318
rxn03901_c0 0.009257971529604133
rxn05326_c0 -0.10355537532764486
rxn05114_c0 0.07320706440309556
rxn03164_c0 0.009257971529604132
rxn00256_c0 -13.991979791673698
rxn08335_c0 0.04957297726805518
rxn06729_c0 0.01851594305920827
rxn00504_c0 -0.05135095786806216
rxn01485_c0 -0.03703188611841653
rxn03031_c0 0.0887651309340192
rxn00239_c0 0.04014774736500163
rxn00441_c0 0.0961533889220579
rxn00302_c0 0.0013852983727637642
rxn03130_c0 0.009257971529604135
rxn01791_c0 0.0009235322485093309
rxn00623_c0 -0.05911737821443292
rxn02507_c0 0.013147829792305764
rxn08043_c0 0.06735161865303811
rxn01029_c0 0.000923532248504836
rxn08131_c0 0.00046176612425031697
rxn14333_c0 0.009257971529604132
rxn01964_c0 0.013147829792305764
rxn02341_c0 0.0009235322485092353
rxn01137_c0 0.002770596745527444
rxn03182_c0 0.009257971529604133
rxn00224_c0 0.0004617661242515749
rxn01513_c0 0.001814052730738549
rxn05333_c0 0.10355537532764489
rxn02186_c0 0.20359856885820407
rxn00209_c0 0.00046176612425026926
rxn02474_c0 -0.000923532248504875
rxn00274_c0 0.12614474432806572
rxn01019_c0 0.06963954833281986
rxn02914_c0 -0.2976378085055958
rxn01603_c0 0.0013852983727637642
rxn00686_c0 -0.0031993511034933042
rxn09232_c0 0.0018140527307267318
rxn01286_c0 0.00715818970995303
rxn05289_c0 0.06274548367590692
rxn01973_c0 0.0887651309340192
rxn00117_c0 0.08479081065574494
rxn05343_c0 0.10355537532764487
rxn01520_c0 0.0018140527307385483
rxn03395_c0 0.00046176612425457924
rxn00330_c0 -13.503902282187829
rxn03445_c0 -0.00046176612425031675
rxn11663_c0 0.0004617661242503168
rxn00493_c0 -0.04304053715028404
rxn00293_c0 0.03703188611841653
rxn14011_c0 0.009257971529604132
rxn21857_c0 -1.1388686639017808e-16
rxn47768_c0 -1.1388686639017805e-16
rxn00154_c0 10.982812283014148
rxn14419_c0 24.304198230714913
rxn08173_c0 43.75259930117939
rxn14412_c0 23.527771723277233
rxn14420_c0 24.304198230714913
rxn14415_c0 15.68518114885149
rxn15949_c0 0.0004617661242515749
rxn41452_c0 -1.1388686639017805e-16
rxn39451_c0 -0.0887651309340192
rxn21858_c0 -1.1388686639017808e-16
rxn46694_c0 -8.430885443645284e-19
rxn16794_c0 8.430885443645283e-19
rxn16776_c0 8.430885443645282e-19
rxn03396_c0 0.00046176612425462385
rxn17275_c0 -0.0036281054614565483
rxn09037_c0 0.001385298372755119
rxn43581_c0 -0.11292007380768641
rxn27318_c0 -0.003628105461456549
rxn14061_c0 0.009257971529604132
rxn13957_c0 0.009257971529604132
rxn40037_c0 0.0887651309340192
rxn15947_c0 0.0004617661242502694
rxn19704_c0 -0.11292007380768643
rxn05319_c0 -5.249341878055617
rxn05195_c0 0.0018470644970062997
rxn01208_c0 -0.10456245768786578
rxn02989_c0 1.886830162271417e-16
rxn05468_c0 20.00000000021212
rxn05467_c0 -24.930034405697096
rxn08333_c0 0.0009235322485004914
rxn02898_c0 0.0009235322485004914
rxn10336_c0 0.007158189709953028
rxn00068_c0 -0.0006926491863773624
rxn05522_c0 0.0004617661242515749
rxn05039_c0 0.0009235322485048757
rxn03536_c0 0.0004617661242503182
rxn03397_c0 0.00046176612425462385
rxn00979_c0 0.0013852983727637644
rxn11703_c0 0.0009235322485091654
rxn03537_c0 0.00046176612425157486
rxn10094_c0 0.00046176612425157486
rxn00333_c0 0.0013852983727637644
rxn03150_c0 0.000461766124251575
rxn03087_c0 -0.0887651309340192
rxn03538_c0 0.00046176612425157486
rxn01213_c0 0.01064326990235925
rxn01265_c0 -0.00046176612425457837
rxn00599_c0 0.0073882579880386896
rxn11702_c0 0.0009235322485091654
rxn05214_c0 0.0004617661242515749
rxn00346_c0 0.0009235322485093309
rxn02897_c0 0.0004617661242515749
rxn02831_c0 0.0009235322485004914
rxn01258_c0 0.0009235322485091654
rxn02832_c0 -0.0009235322485091653
rxn00467_c0 -0.06963954833281985
rxn08234_c0 0.00046176612425157486
rxn05211_c0 -0.0009235322485091648
rxn09429_c0 0.05726551767962423
rxn12376_c0 -0.0004617661242503169
rxn09310_c0 0.000461766124250317
rxn02304_c0 0.0002308830621272907
rxn02185_c0 -0.20359856885820407
rxn04656_c0 17.59245362705189
rxn04657_c0 17.59245362705189
rxn04659_c0 17.59245362705189
rxn02226_c0 17.592453627051892
rxn04660_c0 17.59245362705189
rxn04658_c0 17.59245362705189
rxn00317_c0 17.592453627051892
bio1_biomass 0.28859649325864234
EX_cpd10516_e0 -0.0018470644970062997
EX_cpd00030_e0 -0.00046176612425465107
EX_cpd00099_e0 -0.00046176612425157486
EX_cpd00011_e0 24.930034405697096
EX_cpd00001_e0 5.249341878055617
EX_cpd00063_e0 -0.00046176612425465107
EX_cpd00058_e0 -0.0004617661242503138
EX_cpd00007_e0 -20.0
EX_cpd00009_e0 -0.19075351725153805
EX_cpd00048_e0 -0.05957914433868449
EX_cpd00034_e0 -0.00046176612425465107
EX_cpd00149_e0 -0.00046176612425465107
EX_cpd00205_e0 -0.0004617661242515749
EX_cpd00013_e0 -2.3066699767773606
EX_cpd00971_e0 -5.078889964292577e-12
EX_cpd15378_e0 0.0004617661242503169
EX_cpd00254_e0 -0.00046176612425465107
DM_cpd11416_c0 0.28859649325864234

EX_cpd00007_e0 looks suspicious

hgscott commented 9 months ago

First, I looked at the exchange reactions:

ID Compound Name Flux
EX_cpd10516_e0 Iron -0.0018470644970062997
EX_cpd00030_e0 Mn2+ -0.00046176612425465107
EX_cpd00099_e0 Cl- -0.00046176612425157486
EX_cpd00011_e0 CO2 24.930034405697096
EX_cpd00001_e0 H2O 5.249341878055617
EX_cpd00063_e0 Ca2+ -0.00046176612425465107
EX_cpd00058_e0 Cu2+ -0.0004617661242503138
EX_cpd00007_e0 O2 -20.0
EX_cpd00009_e0 Phosphate -0.19075351725153805
EX_cpd00048_e0 Sulfate -0.05957914433868449
EX_cpd00034_e0 Zn2+ -0.00046176612425465107
EX_cpd00149_e0 Co2+ -0.00046176612425465107
EX_cpd00205_e0 K+ -0.0004617661242515749
EX_cpd00013_e0 NH4+ -2.3066699767773606
EX_cpd00971_e0 Na+ -5.078889964292577e-12
EX_cpd15378_e0 Mg2+ 0.0004617661242503169
EX_cpd00254_e0 Ni2+ -0.00046176612425465107

It really doesn't look like it's taking up any carbon.

hgscott commented 9 months ago

This could be related to #20

hgscott commented 5 months ago

I ran it on my non-gap filled model, and got no growth.

Going to close this issue, since this will come back up when I do gap filling, and I have a way to test for it easily.