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 : udpLa4n_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b1478 b0474 b2518 b1241 b2744 b1278 b4152 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b2690 b1759 b2440 b4374 b4161 b0675 b2361 b2291 b0822 b4138 b4123 b0621 b2913 b2197 b3918 b0418 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.601452 (mmol/gDw/h)
  Minimum Production Rate : 0.317654 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.024200
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.666324
  EX_pi_e : 1.215472
  EX_so4_e : 0.151458
  EX_k_e : 0.117399
  EX_fe2_e : 0.009660
  EX_mg2_e : 0.005218
  EX_ca2_e : 0.003131
  EX_cl_e : 0.003131
  EX_cu2_e : 0.000426
  EX_mn2_e : 0.000416
  EX_zn2_e : 0.000205
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.585082
  EX_co2_e : 26.354338
  EX_h_e : 7.782210
  EX_ac_e : 0.783719
  EX_succ_e : 0.627190
  Auxiliary production reaction : 0.317654
  EX_ura_e : 0.108865
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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