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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b2297 b2458 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0207 b3012 b1982 b0477 b4139 b4015 b0261 b2799 b1602 b0153 b2913 b2406 b0529 b2492 b0904 b2954 b1781 b3001 b3035 b1380 b0325 b1771 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445854 (mmol/gDw/h)
  Minimum Production Rate : 0.187121 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.858971
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.125040
  EX_pi_e : 0.804317
  EX_so4_e : 0.112275
  EX_k_e : 0.087028
  EX_mg2_e : 0.003868
  EX_fe2_e : 0.003680
  EX_fe3_e : 0.003481
  EX_cl_e : 0.002321
  EX_ca2_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.951630
  EX_co2_e : 37.250040
  EX_h_e : 5.108226
  EX_ac_e : 0.259570
  Auxiliary production reaction : 0.187121
  DM_5drib_c : 0.000299
  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.

Last updated: 21-Sep-2023
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