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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2925 b2097 b3617 b0160 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0675 b2361 b4381 b2406 b0511 b0114 b1539 b2492 b0904 b1533 b0516 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.521279 (mmol/gDw/h)
  Minimum Production Rate : 0.379099 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.472460
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.527388
  EX_pi_e : 0.502829
  EX_so4_e : 0.131269
  EX_k_e : 0.101750
  EX_fe2_e : 0.008372
  EX_mg2_e : 0.004522
  EX_ca2_e : 0.002713
  EX_cl_e : 0.002713
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000360
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.342590
  EX_co2_e : 25.767822
  EX_h_e : 10.280406
  EX_ac_e : 1.213968
  EX_his__L_e : 1.154185
  Auxiliary production reaction : 0.379099
  EX_xan_e : 0.013991
  DM_mththf_c : 0.000234
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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