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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b2836 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2779 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b0411 b1602 b0114 b0529 b2492 b0904 b1380 b2660 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.394099 (mmol/gDw/h)
  Minimum Production Rate : 0.640825 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.656956
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.460359
  EX_pi_e : 1.661800
  EX_fe3_e : 0.197458
  EX_so4_e : 0.099242
  EX_k_e : 0.076925
  EX_mg2_e : 0.003419
  EX_ca2_e : 0.002051
  EX_cl_e : 0.002051
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 54.078258
  EX_co2_e : 35.439203
  EX_h_e : 6.381895
  EX_acald_e : 0.987858
  Auxiliary production reaction : 0.640825
  EX_fe2_e : 0.191128
  EX_mththf_e : 0.000177
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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