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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b3399 b4069 b2502 b2744 b0871 b2297 b2458 b2925 b2097 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2690 b1982 b4139 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b3927 b3029 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356980 (mmol/gDw/h)
  Minimum Production Rate : 0.107215 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.023538
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.177003
  EX_pi_e : 0.451561
  EX_so4_e : 0.089895
  EX_k_e : 0.069680
  EX_fe3_e : 0.005733
  EX_mg2_e : 0.003097
  EX_ca2_e : 0.001858
  EX_cl_e : 0.001858
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.425364
  EX_co2_e : 28.000802
  EX_h_e : 9.065744
  EX_pyr_e : 5.357274
  EX_ac_e : 0.207829
  Auxiliary production reaction : 0.107215
  EX_glyclt_e : 0.000399
  DM_5drib_c : 0.000240
  DM_4crsol_c : 0.000080

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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