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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2925 b2097 b3617 b0030 b2407 b3236 b1779 b2690 b2210 b3665 b0675 b0411 b0822 b4381 b3654 b3714 b3664 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.304825 (mmol/gDw/h)
  Minimum Production Rate : 1.169198 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.101976
  EX_o2_e : 285.636175
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.630486
  EX_pi_e : 2.632433
  EX_so4_e : 0.076761
  EX_k_e : 0.059500
  EX_mg2_e : 0.002644
  EX_ca2_e : 0.001587
  EX_cl_e : 0.001587
  EX_cu2_e : 0.000216
  EX_mn2_e : 0.000211
  EX_zn2_e : 0.000104
  EX_ni2_e : 0.000098

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995104
  EX_h2o_e : 552.519441
  EX_co2_e : 35.118704
  Auxiliary production reaction : 1.169198
  EX_ac_e : 0.923072
  DM_mththf_c : 0.000137
  DM_5drib_c : 0.000069
  DM_4crsol_c : 0.000068

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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