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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b0512 b2297 b2458 b2779 b3236 b2883 b1982 b3616 b3589 b2210 b0675 b2361 b0411 b4388 b4381 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.489577 (mmol/gDw/h)
  Minimum Production Rate : 0.462890 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.522091
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.968844
  EX_pi_e : 1.398028
  EX_so4_e : 0.123285
  EX_k_e : 0.095562
  EX_fe2_e : 0.007863
  EX_mg2_e : 0.004247
  EX_ca2_e : 0.002548
  EX_cl_e : 0.002548
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.805583
  EX_co2_e : 25.750102
  EX_h_e : 10.675887
  EX_ac_e : 2.421782
  Auxiliary production reaction : 0.462890
  EX_alltn_e : 0.013140
  DM_mththf_c : 0.000219
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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