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 : udpglcur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b3831 b3614 b0910 b3752 b4152 b2925 b2097 b2926 b2781 b1612 b1611 b4122 b2690 b1759 b0675 b0411 b0822 b4138 b4123 b0621 b2913 b4381 b1727 b0529 b2197 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449194 (mmol/gDw/h)
  Minimum Production Rate : 0.237204 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.411829
  EX_o2_e : 279.560663
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.488353
  EX_pi_e : 0.907703
  EX_so4_e : 0.113116
  EX_k_e : 0.087680
  EX_mg2_e : 0.003897
  EX_ca2_e : 0.002338
  EX_cl_e : 0.002338
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992785
  EX_h2o_e : 544.677364
  EX_co2_e : 29.571827
  EX_ac_e : 3.116859
  EX_succ_e : 0.468416
  Auxiliary production reaction : 0.237204
  EX_ura_e : 0.081342
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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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