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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b2836 b3399 b2744 b3708 b3008 b0871 b2779 b2925 b2097 b0160 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b0675 b2361 b2291 b0261 b1602 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2413 b3447 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354288 (mmol/gDw/h)
  Minimum Production Rate : 0.243968 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.003454
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.314610
  EX_pi_e : 0.829676
  EX_so4_e : 0.089218
  EX_k_e : 0.069155
  EX_fe2_e : 0.005692
  EX_mg2_e : 0.003073
  EX_ca2_e : 0.001844
  EX_cl_e : 0.001844
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 39.274158
  EX_co2_e : 27.965876
  EX_h_e : 8.598418
  EX_glyc__R_e : 5.098317
  Auxiliary production reaction : 0.243964
  DM_oxam_c : 0.000396
  DM_5drib_c : 0.000238
  DM_4crsol_c : 0.000079

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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