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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b4069 b4384 b3115 b1849 b2296 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b1602 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b2660 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.490003 (mmol/gDw/h)
  Minimum Production Rate : 0.042852 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.927480
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.506255
  EX_pi_e : 0.558365
  EX_so4_e : 0.123393
  EX_k_e : 0.095645
  EX_fe2_e : 0.007870
  EX_mg2_e : 0.004251
  EX_cl_e : 0.002550
  EX_ca2_e : 0.002550
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.384162
  EX_co2_e : 38.887452
  EX_h_e : 4.959027
  EX_ac_e : 0.285273
  Auxiliary production reaction : 0.042852
  DM_mththf_c : 0.000220
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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