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 : lald__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b1478 b1241 b4069 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1033 b1602 b0153 b2492 b0904 b0591 b1380 b2660 b1771 b1518 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.502071 (mmol/gDw/h)
  Minimum Production Rate : 0.445156 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.177079
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.422328
  EX_pi_e : 0.484301
  EX_so4_e : 0.126432
  EX_k_e : 0.098001
  EX_fe2_e : 0.008064
  EX_mg2_e : 0.004355
  EX_ca2_e : 0.002613
  EX_cl_e : 0.002613
  EX_cu2_e : 0.000356
  EX_mn2_e : 0.000347
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.729404
  EX_co2_e : 37.471088
  EX_h_e : 4.905531
  Auxiliary production reaction : 0.445156
  EX_ac_e : 0.292299
  DM_mththf_c : 0.000225
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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