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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b2926 b3844 b1004 b3713 b1109 b0046 b2690 b2463 b0207 b3012 b2210 b3551 b2799 b1602 b4219 b1832 b1778 b4381 b2492 b0904 b1781 b3001 b1380 b0325 b1710 b2480 b1771 b1206 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410582 (mmol/gDw/h)
  Minimum Production Rate : 0.165392 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.263769
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.434249
  EX_pi_e : 0.726835
  EX_so4_e : 0.103393
  EX_k_e : 0.080143
  EX_fe2_e : 0.006594
  EX_mg2_e : 0.003562
  EX_ca2_e : 0.002137
  EX_cl_e : 0.002137
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.140038
  EX_co2_e : 37.801529
  EX_h_e : 4.837880
  EX_3hpp_e : 1.230683
  Auxiliary production reaction : 0.165392
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000092

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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