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 (31 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1238 b2797 b3117 b1814 b4471 b2440 b3665 b4381 b2239 b2406 b0112 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397320 (mmol/gDw/h)
  Minimum Production Rate : 0.396666 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.518850
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.067680
  EX_pi_e : 1.573255
  EX_so4_e : 0.496719
  EX_k_e : 0.077554
  EX_fe2_e : 0.006381
  EX_mg2_e : 0.003447
  EX_cl_e : 0.002068
  EX_ca2_e : 0.002068
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 48.387170
  EX_co2_e : 29.565071
  EX_h_e : 7.342017
  EX_ac_e : 2.104622
  Auxiliary production reaction : 0.396666
  EX_mththf_e : 0.000178
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000089

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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