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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b2836 b3553 b4382 b4069 b4384 b3708 b3926 b2297 b2458 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b1602 b2913 b2406 b0114 b0509 b3125 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430495 (mmol/gDw/h)
  Minimum Production Rate : 0.182322 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.055679
  EX_o2_e : 285.466891
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.927495
  EX_pi_e : 0.962224
  EX_so4_e : 0.108407
  EX_k_e : 0.084030
  EX_mg2_e : 0.003735
  EX_ca2_e : 0.002241
  EX_cl_e : 0.002241
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993086
  EX_h2o_e : 551.219387
  EX_co2_e : 36.378612
  EX_12ppd__R_e : 0.539381
  EX_ac_e : 0.250628
  Auxiliary production reaction : 0.182322
  EX_hxan_e : 0.000482
  DM_5drib_c : 0.000289
  DM_4crsol_c : 0.000096

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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