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 (65 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1478 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b2930 b4232 b3697 b3925 b2297 b2458 b2407 b3236 b2690 b1982 b3616 b3589 b2210 b0675 b0261 b0822 b2868 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452015 (mmol/gDw/h)
  Minimum Production Rate : 0.157541 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.777544
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.513101
  EX_pi_e : 0.436016
  EX_so4_e : 0.113826
  EX_k_e : 0.088230
  EX_fe2_e : 0.007260
  EX_mg2_e : 0.003921
  EX_ca2_e : 0.002353
  EX_cl_e : 0.002353
  EX_cu2_e : 0.000320
  EX_mn2_e : 0.000312
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.036983
  EX_co2_e : 30.946967
  EX_h_e : 5.937798
  EX_ac_e : 1.153126
  EX_hxan_e : 0.157845
  Auxiliary production reaction : 0.157541
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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