MetNetComp Database [1] / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iNF517 [2].
Target metabolite : citr__L_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 177
  Remaining genes: LLMG_RS04525 LLMG_RS10345 LLMG_RS05745 LLMG_RS05965 LLMG_RS06010 LLMG_RS11690 LLMG_RS04745 LLMG_RS05335 LLMG_RS07450 LLMG_RS07455 LLMG_RS12215 LLMG_RS05125 LLMG_RS08920 LLMG_RS08940 LLMG_RS09820 LLMG_RS08930 LLMG_RS08925 LLMG_RS00670 LLMG_RS01855 LLMG_RS00675 LLMG_RS08570 LLMG_RS09540 LLMG_RS11480 LLMG_RS02815 LLMG_RS08950 LLMG_RS05245 LLMG_RS05235 LLMG_RS05240 LLMG_RS06580 LLMG_RS04750 LLMG_RS04740 LLMG_RS11595 LLMG_RS06585 LLMG_RS11835 LLMG_RS05265 LLMG_RS11600 LLMG_RS05980 LLMG_RS10255 LLMG_RS03160 LLMG_RS03390 LLMG_RS02185 LLMG_RS12590 LLMG_RS10095 LLMG_RS00635 LLMG_RS02010 LLMG_RS08750 LLMG_RS01995 LLMG_RS12445 LLMG_RS11115 LLMG_RS08955 LLMG_RS09740 LLMG_RS09760 LLMG_RS09745 LLMG_RS09735 LLMG_RS09750 LLMG_RS12095 LLMG_RS09765 LLMG_RS09755 LLMG_RS09730 LLMG_RS08760 LLMG_RS09640 LLMG_RS02820 LLMG_RS08945 LLMG_RS10800 LLMG_RS10795 LLMG_RS12465 LLMG_RS06195 LLMG_RS09680 LLMG_RS08860 LLMG_RS02170 LLMG_RS07830 LLMG_RS03945 LLMG_RS12260 LLMG_RS08520 LLMG_RS02375 LLMG_RS07415 LLMG_RS07425 LLMG_RS05685 LLMG_RS04645 LLMG_RS10195 LLMG_RS01240 LLMG_RS03780 LLMG_RS07495 LLMG_RS00665 LLMG_RS06170 LLMG_RS06165 LLMG_RS06175 LLMG_RS01465 LLMG_RS06160 LLMG_RS11000 LLMG_RS12615 LLMG_RS12105 LLMG_RS10365 LLMG_RS08440 LLMG_RS05680 LLMG_RS08710 LLMG_RS10005 LLMG_RS08705 LLMG_RS03285 LLMG_RS03735 LLMG_RS02290 LLMG_RS09705 LLMG_RS09635 LLMG_RS02600 LLMG_RS11990 LLMG_RS01845 LLMG_RS01325 LLMG_RS07955 LLMG_RS04035 LLMG_RS11155 LLMG_RS09700 LLMG_RS01095 LLMG_RS11025 LLMG_RS11030 LLMG_RS01110 LLMG_RS08500 LLMG_RS03290 LLMG_RS01105 LLMG_RS09515 LLMG_RS02175 LLMG_RS09495 LLMG_RS09510 LLMG_RS09500 LLMG_RS09490 LLMG_RS10900 LLMG_RS04050 LLMG_RS09505 LLMG_RS02180 LLMG_RS02125 LLMG_RS04440 LLMG_RS05370 LLMG_RS10075 LLMG_RS02890 LLMG_RS10000 LLMG_RS02840 LLMG_RS07185 LLMG_RS09645 LLMG_RS03215 LLMG_RS05270 LLMG_RS08000 LLMG_RS10835 LLMG_RS05280 LLMG_RS05285 LLMG_RS00430 LLMG_RS02055 LLMG_RS07395 LLMG_RS02630 LLMG_RS04660 LLMG_RS04655 LLMG_RS11610 LLMG_RS06735 LLMG_RS12110 LLMG_RS05635 LLMG_RS11200 LLMG_RS01860 LLMG_RS10940 LLMG_RS04555 LLMG_RS11470 LLMG_RS12325 LLMG_RS06815 LLMG_RS06820 LLMG_RS03760 LLMG_RS08030 LLMG_RS10360 LLMG_RS01090 LLMG_RS05655 LLMG_RS04530 LLMG_RS12290 LLMG_RS05650 LLMG_RS02785 LLMG_RS07630 LLMG_RS02930 LLMG_RS10780 LLMG_RS12480 LLMG_RS00930 LLMG_RS00940 LLMG_RS00935   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.025323 (mmol/gDw/h)
  Minimum Production Rate : 0.005532 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 1.573385
  EX_h2o_e : 0.444615
  EX_thr__L_e : 0.060000
  EX_glu__L_e : 0.050000
  EX_ser__L_e : 0.040000
  EX_ala__L_e : 0.020575
  EX_pi_e : 0.017458
  EX_ile__L_e : 0.012300
  EX_arg__L_e : 0.010000
  EX_asp__L_e : 0.010000
  EX_leu__L_e : 0.010000
  EX_val__L_e : 0.010000
  EX_lys__L_e : 0.009004
  EX_cys__L_e : 0.005218
  EX_phe__L_e : 0.004255
  EX_ura_e : 0.003836
  EX_xan_e : 0.003003
  EX_ade_e : 0.002822
  EX_met__L_e : 0.002128
  EX_his__L_e : 0.001915
  EX_thymd_e : 0.000600
  EX_nac_e : 0.000051

Product: (mmol/gDw/h)
  EX_h_e : 3.805303
  EX_for_e : 1.782283
  EX_etoh_e : 1.020000
  EX_lac__L_e : 0.920000
  EX_ac_e : 0.830000
  EX_pyr_e : 0.391322
  EX_nh4_e : 0.062320
  EX_pro__L_e : 0.030000
  EX_co2_e : 0.016754
  EX_tyr__L_e : 0.006520
  EX_2mbald_e : 0.006130
  Auxiliary production reaction : 0.005532
  EX_2h3mb_e : 0.002234
  EX_akg_e : 0.000710
  EX_2hxic__L_e : 0.000638

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 27-Sep-2023
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