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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b1779 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b4381 b0452 b0114 b2366 b2492 b0904 b1533 b3927 b0516 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.700942 (mmol/gDw/h)
  Minimum Production Rate : 0.025220 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.981981
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.023657
  EX_pi_e : 0.751791
  EX_so4_e : 0.277389
  EX_k_e : 0.136819
  EX_mobd_e : 0.025224
  EX_fe2_e : 0.011258
  EX_mg2_e : 0.006081
  EX_ca2_e : 0.003648
  EX_cl_e : 0.003648
  EX_cu2_e : 0.000497
  EX_mn2_e : 0.000484
  EX_zn2_e : 0.000239
  EX_ni2_e : 0.000226
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 50.147434
  EX_co2_e : 30.396148
  EX_h_e : 6.591443
  Auxiliary production reaction : 0.025220
  EX_alltn_e : 0.018813
  DM_mththf_c : 0.000314
  DM_5drib_c : 0.000158
  DM_4crsol_c : 0.000156

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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