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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2066 b0474 b2518 b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b3617 b2407 b3124 b0907 b2498 b2868 b0114 b0755 b3612 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391351 (mmol/gDw/h)
  Minimum Production Rate : 0.500184 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.726920
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.228345
  EX_pi_e : 1.377867
  EX_so4_e : 0.098550
  EX_k_e : 0.076389
  EX_fe2_e : 0.006285
  EX_mg2_e : 0.003395
  EX_cl_e : 0.002037
  EX_ca2_e : 0.002037
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 51.900115
  EX_co2_e : 35.561045
  EX_h_e : 6.783377
  EX_ac_e : 1.685884
  Auxiliary production reaction : 0.500184
  EX_hxan_e : 0.000263
  DM_mththf_c : 0.000175
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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