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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b3752 b4152 b2781 b1612 b1611 b4122 b0907 b1759 b4161 b4138 b4123 b0621 b2406 b2197 b2835 b3918 b1912 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.535094 (mmol/gDw/h)
  Minimum Production Rate : 0.029732 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.199841
  EX_o2_e : 282.088325
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.537894
  EX_pi_e : 0.516155
  EX_so4_e : 0.134747
  EX_k_e : 0.104447
  EX_mg2_e : 0.004642
  EX_ca2_e : 0.002785
  EX_cl_e : 0.002785
  EX_cu2_e : 0.000379
  EX_mn2_e : 0.000370
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991406
  EX_h2o_e : 549.798039
  EX_co2_e : 32.889630
  EX_succ_e : 0.557992
  EX_ura_e : 0.379461
  Auxiliary production reaction : 0.029732
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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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