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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b2836 b4069 b4384 b3708 b3752 b3926 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b1982 b4139 b2797 b3117 b1814 b4471 b0261 b1602 b4381 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b3029 b1380 b2660 b0514 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442429 (mmol/gDw/h)
  Minimum Production Rate : 0.281117 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.411387
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.183778
  EX_pi_e : 0.426769
  EX_so4_e : 0.111412
  EX_k_e : 0.086359
  EX_fe2_e : 0.007106
  EX_mg2_e : 0.003838
  EX_ca2_e : 0.002303
  EX_cl_e : 0.002303
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.006527
  EX_co2_e : 38.793155
  EX_h_e : 5.728868
  Auxiliary production reaction : 0.281117
  EX_ac_e : 0.257576
  EX_glyclt_e : 0.000495
  DM_5drib_c : 0.000297
  DM_4crsol_c : 0.000099

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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