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 (63 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b0474 b2518 b2744 b1278 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b4374 b4161 b0675 b3945 b4388 b4138 b4123 b0621 b4381 b0529 b2197 b3918 b0418 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449782 (mmol/gDw/h)
  Minimum Production Rate : 0.237550 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.413747
  EX_o2_e : 279.546724
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.495528
  EX_pi_e : 0.908962
  EX_so4_e : 0.113264
  EX_k_e : 0.087794
  EX_mg2_e : 0.003902
  EX_cl_e : 0.002341
  EX_ca2_e : 0.002341
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992776
  EX_h2o_e : 544.683335
  EX_co2_e : 29.557867
  EX_ac_e : 3.107824
  EX_succ_e : 0.469029
  Auxiliary production reaction : 0.237550
  EX_ura_e : 0.081412
  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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