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 (31 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b2836 b1478 b3942 b1732 b1241 b4069 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b3551 b0261 b2799 b3945 b1602 b2223 b4219 b1832 b1778 b4381 b3915 b0529 b2492 b0904 b1380 b1710 b2480 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.436963 (mmol/gDw/h)
  Minimum Production Rate : 0.578238 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.786953
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.440969
  EX_pi_e : 0.999736
  EX_so4_e : 0.110036
  EX_k_e : 0.085292
  EX_fe3_e : 0.007018
  EX_mg2_e : 0.003791
  EX_ca2_e : 0.002274
  EX_cl_e : 0.002274
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.343730
  EX_co2_e : 35.934190
  EX_h_e : 5.998208
  Auxiliary production reaction : 0.578238
  EX_hxan_e : 0.430450
  EX_ac_e : 0.254394
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000097

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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