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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b1478 b0474 b2518 b1241 b0351 b3831 b4069 b4384 b3708 b3115 b1849 b2296 b2779 b2925 b2097 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b0822 b2406 b0114 b2366 b2492 b0904 b1533 b3927 b2835 b0516 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.648161 (mmol/gDw/h)
  Minimum Production Rate : 0.274945 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.331559
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.101613
  EX_pi_e : 0.900166
  EX_so4_e : 0.163220
  EX_k_e : 0.126517
  EX_fe2_e : 0.010410
  EX_mg2_e : 0.005623
  EX_ca2_e : 0.003374
  EX_cl_e : 0.003374
  EX_cu2_e : 0.000460
  EX_mn2_e : 0.000448
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000209
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 50.032205
  EX_co2_e : 29.888604
  EX_h_e : 7.434441
  EX_ac_e : 0.377350
  Auxiliary production reaction : 0.274945
  EX_alltn_e : 0.000436
  DM_mththf_c : 0.000290
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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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