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 (26 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b1479 b3115 b1849 b2296 b2926 b3617 b3844 b3124 b3236 b2463 b3962 b0104 b2210 b4267 b3551 b1014 b3945 b4388 b4219 b1832 b1778 b2975 b0114 b3603 b0306 b1539 b3605 b3927 b3821 b1380 b0325 b1710 b2480 b0508 b0514 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.556841 (mmol/gDw/h)
  Minimum Production Rate : 0.095992 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.167121
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.013833
  EX_pi_e : 0.537132
  EX_so4_e : 0.140224
  EX_k_e : 0.108691
  EX_fe2_e : 0.008943
  EX_mg2_e : 0.004831
  EX_ca2_e : 0.002898
  EX_cl_e : 0.002898
  EX_cu2_e : 0.000395
  EX_mn2_e : 0.000385
  EX_zn2_e : 0.000190
  EX_ni2_e : 0.000180
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.059961
  EX_co2_e : 34.259345
  EX_h_e : 6.558832
  EX_ac_e : 1.250187
  Auxiliary production reaction : 0.095992
  EX_glyc__R_e : 0.000186
  DM_5drib_c : 0.000125
  DM_4crsol_c : 0.000124

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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