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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b3831 b4384 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4161 b4388 b4138 b4123 b0621 b2239 b2406 b0755 b3612 b0529 b2197 b2835 b3918 b1912 b1813 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.617677 (mmol/gDw/h)
  Minimum Production Rate : 0.160071 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.218830
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.546911
  EX_pi_e : 0.915957
  EX_so4_e : 0.155543
  EX_k_e : 0.120566
  EX_fe2_e : 0.009921
  EX_mg2_e : 0.005358
  EX_cl_e : 0.003215
  EX_ca2_e : 0.003215
  EX_cu2_e : 0.000438
  EX_mn2_e : 0.000427
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.343538
  EX_co2_e : 28.557874
  EX_h_e : 7.519591
  EX_succ_e : 0.644109
  EX_ura_e : 0.277954
  Auxiliary production reaction : 0.160071
  DM_5drib_c : 0.000139
  DM_4crsol_c : 0.000138

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.

Last updated: 21-Sep-2023
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