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 : 5dglcn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 7
  Gene deletion: STM1290 STM3068 STM2141 STM0974 STM0152 STM4484 STM2317   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.298290 (mmol/gDw/h)
  Minimum Production Rate : 0.008625 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.287194
  EX_pi_e : 0.264530
  EX_k_e : 0.052976
  EX_so4_e : 0.036386
  EX_mg2_e : 0.002355
  EX_fe2_e : 0.002186
  EX_ca2_e : 0.001413
  EX_cl_e : 0.001413
  EX_cu2_e : 0.000942
  EX_mn2_e : 0.000942
  EX_mobd_e : 0.000942
  EX_zn2_e : 0.000942
  EX_cobalt2_e : 0.000942

Product: (mmol/gDw/h)
  EX_h2o_e : 26.641571
  EX_co2_e : 18.409601
  EX_h_e : 2.537413
  EX_5dglcn_e : 0.008625
  DM_hmfurn_c : 0.000133

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, 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: 27-Sep-2023
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