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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0945 b4069 b4384 b2744 b3708 b3008 b2297 b2458 b0030 b2407 b2797 b3117 b1814 b4471 b3665 b0411 b4381 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b2947 b0591 b2578 b1533 b3927 b3821 b0723 b4141 b1798 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.711439 (mmol/gDw/h)
  Minimum Production Rate : 0.181360 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.274428
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.952996
  EX_pi_e : 1.230337
  EX_so4_e : 0.360514
  EX_k_e : 0.138868
  EX_fe2_e : 0.011426
  EX_mg2_e : 0.006172
  EX_ca2_e : 0.003703
  EX_cl_e : 0.003703
  EX_cu2_e : 0.000504
  EX_mn2_e : 0.000492
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.324613
  EX_co2_e : 24.856377
  EX_h_e : 8.147154
  EX_ac_e : 0.595549
  EX_succ_e : 0.235271
  Auxiliary production reaction : 0.181360
  EX_mththf_e : 0.000319
  DM_5drib_c : 0.000160
  DM_4crsol_c : 0.000159

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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