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 : cph4_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3500 b3399 b4382 b0474 b2518 b4384 b2744 b3708 b3008 b3752 b0871 b2781 b0099 b0160 b2235 b2883 b1982 b2797 b3117 b1814 b4471 b1623 b0411 b0452 b0114 b2366 b2492 b0904 b2954 b1533 b3927 b1517 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.782211 (mmol/gDw/h)
  Minimum Production Rate : 0.179885 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.501767
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.347234
  EX_pi_e : 0.754525
  EX_so4_e : 0.196976
  EX_k_e : 0.152682
  EX_mg2_e : 0.006786
  EX_fe2_e : 0.006456
  EX_fe3_e : 0.006108
  EX_ca2_e : 0.004071
  EX_cl_e : 0.004071
  EX_cu2_e : 0.000555
  EX_mn2_e : 0.000541
  EX_zn2_e : 0.000267
  EX_ni2_e : 0.000253
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 49.084712
  EX_co2_e : 26.632894
  EX_h_e : 8.272681
  Auxiliary production reaction : 0.179885
  DM_mththf_c : 0.000350
  DM_5drib_c : 0.000176
  DM_4crsol_c : 0.000174

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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