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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b2297 b2458 b2779 b2925 b2097 b2407 b2690 b3616 b3589 b0675 b0822 b4388 b4381 b0511 b1727 b0114 b0529 b2492 b0904 b0515 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.335069 (mmol/gDw/h)
  Minimum Production Rate : 0.428250 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 39.217728
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.332617
  EX_pi_e : 1.179710
  EX_so4_e : 0.084377
  EX_k_e : 0.065403
  EX_fe2_e : 0.005382
  EX_mg2_e : 0.002907
  EX_ca2_e : 0.001744
  EX_cl_e : 0.001744
  EX_cu2_e : 0.000238
  EX_mn2_e : 0.000232
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 53.064811
  EX_co2_e : 39.075539
  EX_h_e : 5.807865
  EX_ac_e : 1.443355
  Auxiliary production reaction : 0.428250
  EX_xan_e : 0.000226
  DM_mththf_c : 0.000150
  EX_glyc__R_e : 0.000112
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000075

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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