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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b1004 b3713 b1109 b0046 b2463 b2210 b3551 b2799 b3945 b1602 b4219 b1832 b1778 b3915 b0755 b3612 b0529 b1380 b1710 b2480 b1695 b1206 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.582456 (mmol/gDw/h)
  Minimum Production Rate : 0.424446 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.574229
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.290470
  EX_pi_e : 0.561840
  EX_so4_e : 0.146674
  EX_k_e : 0.113691
  EX_fe3_e : 0.009355
  EX_mg2_e : 0.005053
  EX_ca2_e : 0.003032
  EX_cl_e : 0.003032
  EX_cu2_e : 0.000413
  EX_mn2_e : 0.000402
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.195902
  EX_co2_e : 34.395094
  EX_h_e : 6.210080
  Auxiliary production reaction : 0.424446
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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