MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b2836 b3399 b1241 b0351 b3831 b4069 b2502 b4384 b2744 b3708 b3008 b0910 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b0651 b2162 b1779 b2690 b1982 b2688 b2797 b3117 b1814 b4471 b0596 b3665 b0675 b2361 b0261 b0822 b0507 b3709 b3161 b0112 b1727 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b4042 b1473 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376016 (mmol/gDw/h)
  Minimum Production Rate : 0.075097 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.680307
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.875100
  EX_pi_e : 0.587998
  EX_so4_e : 0.169785
  EX_k_e : 0.073396
  EX_fe2_e : 0.006039
  EX_mg2_e : 0.003262
  EX_ca2_e : 0.001957
  EX_cl_e : 0.001957
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 44.602854
  EX_co2_e : 32.376126
  EX_h_e : 8.840770
  EX_ac_e : 4.796916
  EX_thym_e : 0.143187
  Auxiliary production reaction : 0.075097
  EX_ade_e : 0.000421
  DM_5drib_c : 0.000252
  DM_4crsol_c : 0.000084

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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: 21-Sep-2023
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