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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b4069 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1602 b4381 b3654 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b0516 b1771 b1518 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459015 (mmol/gDw/h)
  Minimum Production Rate : 0.159311 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.886423
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.594571
  EX_fe3_e : 1.934305
  EX_pi_e : 0.602080
  EX_so4_e : 0.115589
  EX_k_e : 0.089597
  EX_mg2_e : 0.003982
  EX_cl_e : 0.002389
  EX_ca2_e : 0.002389
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.937519
  EX_co2_e : 39.030926
  EX_h_e : 7.056398
  EX_fe2_e : 1.926933
  EX_ac_e : 0.267232
  Auxiliary production reaction : 0.159311
  DM_mththf_c : 0.000206
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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