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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3942 b1732 b0474 b2518 b1241 b0351 b3708 b3008 b1479 b3752 b0871 b2297 b2458 b2925 b2097 b2926 b3617 b2407 b3236 b2883 b2690 b2463 b2797 b3117 b1814 b4471 b2210 b3551 b0261 b3945 b4219 b1832 b1778 b4381 b2406 b0452 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b1710 b2480 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.347728 (mmol/gDw/h)
  Minimum Production Rate : 0.079915 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.447259
  EX_o2_e : 280.191792
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.076258
  EX_pi_e : 0.335420
  EX_so4_e : 0.087565
  EX_k_e : 0.067874
  EX_mg2_e : 0.003017
  EX_ca2_e : 0.001810
  EX_cl_e : 0.001810
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994415
  EX_h2o_e : 543.731728
  EX_co2_e : 27.719241
  EX_pyr_e : 5.145286
  EX_fum_e : 0.442990
  EX_ins_e : 0.079915
  EX_ade_e : 0.000234
  DM_5drib_c : 0.000078
  DM_4crsol_c : 0.000078

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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