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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2836 b4382 b1241 b0351 b4384 b0871 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b3946 b2210 b0825 b4015 b2799 b3945 b1602 b3915 b1727 b0755 b3612 b0529 b2492 b0904 b3927 b1380 b2660 b1695 b1517 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369362 (mmol/gDw/h)
  Minimum Production Rate : 0.096835 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.765541
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.990325
  EX_pi_e : 0.453124
  EX_so4_e : 0.093013
  EX_k_e : 0.072097
  EX_fe3_e : 0.005932
  EX_mg2_e : 0.003204
  EX_ca2_e : 0.001923
  EX_cl_e : 0.001923
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 42.544530
  EX_co2_e : 29.319131
  EX_h_e : 7.777272
  EX_pyr_e : 4.376248
  EX_etoh_e : 0.904208
  Auxiliary production reaction : 0.096835
  EX_ade_e : 0.000249
  DM_mththf_c : 0.000165
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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