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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2930 b4232 b3697 b3925 b2297 b2458 b3617 b0030 b2407 b2690 b1982 b0675 b0822 b1727 b0114 b0529 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446863 (mmol/gDw/h)
  Minimum Production Rate : 0.169022 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.647310
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.006990
  EX_pi_e : 0.431046
  EX_so4_e : 0.112529
  EX_k_e : 0.087224
  EX_fe2_e : 0.007177
  EX_mg2_e : 0.003877
  EX_ca2_e : 0.002326
  EX_cl_e : 0.002326
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 45.140004
  EX_co2_e : 31.118528
  EX_h_e : 5.132716
  EX_ac_e : 0.664942
  DM_oxam_c : 0.180911
  DM_mththf_c : 0.180611
  Auxiliary production reaction : 0.169022
  DM_5drib_c : 0.000300
  DM_4crsol_c : 0.000100

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.

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Last updated: 21-Sep-2023
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