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 : prlp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b3399 b1241 b0351 b4069 b2744 b3926 b2297 b2458 b2926 b3617 b0160 b1004 b3713 b1109 b0046 b3236 b1982 b4374 b0675 b2361 b2291 b0261 b1602 b2913 b0114 b0529 b2492 b0904 b1380 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354434 (mmol/gDw/h)
  Minimum Production Rate : 0.165994 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.621703
  EX_o2_e : 283.971724
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.737434
  EX_pi_e : 0.673877
  EX_so4_e : 0.089253
  EX_k_e : 0.069183
  EX_mg2_e : 0.003075
  EX_ca2_e : 0.001845
  EX_cl_e : 0.001845
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994307
  EX_h2o_e : 550.961982
  EX_co2_e : 34.321887
  EX_etoh_e : 1.033814
  EX_his__L_e : 1.026537
  EX_ac_e : 0.206346
  Auxiliary production reaction : 0.165994
  DM_5drib_c : 0.000238
  DM_4crsol_c : 0.000079

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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