MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 101: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM0758 STM4061 STM3646 STM3747 STM3952 STM1749 STM2463 STM2285 STM1522 STM3614 STM3866 STM1885 STM3986 STM3880 STM1135 STM2200 STM0974 STM2472 STM2403 STM0832 STM1211 STM2317 STM3179 STM1480 STM1806 STM0039 STM0700 STM3661 STM2041 STM2051 STM4301 STM3599 STM4325 STM0627 STM3959 STM4456 STM3763   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.016186 (mmol/gDw/h)
  Minimum Production Rate : 0.041621 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.178358
  EX_o2_e : 0.043412
  EX_pi_e : 0.014351
  EX_k_e : 0.002875
  EX_so4_e : 0.001973
  EX_mg2_e : 0.000128
  EX_fe3_e : 0.000119
  EX_ca2_e : 0.000077
  EX_cl_e : 0.000077
  EX_cobalt2_e : 0.000051
  EX_cu2_e : 0.000051
  EX_mn2_e : 0.000051
  EX_mobd_e : 0.000051
  EX_zn2_e : 0.000051

Product: (mmol/gDw/h)
  EX_h_e : 9.865996
  EX_lac__D_e : 9.714686
  EX_h2o_e : 0.488616
  EX_co2_e : 0.077108
  EX_12ppd__R_e : 0.041605
  EX_succ_e : 0.006990

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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 (2023).
[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.

Last updated: 09-Jul-2025
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