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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b1241 b0351 b4069 b3708 b0871 b2297 b2458 b2925 b2097 b3617 b0030 b2407 b1238 b1004 b3713 b1109 b0046 b2690 b2797 b3117 b1814 b4471 b2210 b1033 b0261 b3945 b1602 b4381 b2406 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400922 (mmol/gDw/h)
  Minimum Production Rate : 1.200068 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.635856
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.531339
  EX_pi_e : 1.586800
  EX_so4_e : 0.100960
  EX_k_e : 0.078257
  EX_fe2_e : 0.006439
  EX_mg2_e : 0.003478
  EX_cl_e : 0.002087
  EX_ca2_e : 0.002087
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.121933
  EX_co2_e : 29.449857
  EX_h_e : 7.490437
  Auxiliary production reaction : 1.200068
  EX_ac_e : 0.923186
  EX_pyr_e : 0.481935
  EX_ade_e : 0.000270
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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