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 : 2odecg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM0158 STM1749 STM2463 STM2285 STM3526 STM0169 STM0861 STM4326 STM1511 STM1299 STM2947 STM3709 STM3068 STM2141 STM1135 STM1570 STM4036 STM1448 STM3069 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.166399 (mmol/gDw/h)
  Minimum Production Rate : 0.137205 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.833740
  EX_pi_e : 0.284772
  EX_k_e : 0.029552
  EX_so4_e : 0.020298
  EX_mg2_e : 0.001314
  EX_fe2_e : 0.001220
  EX_ca2_e : 0.000788
  EX_cl_e : 0.000788
  EX_cobalt2_e : 0.000525
  EX_cu2_e : 0.000525
  EX_mn2_e : 0.000525
  EX_mobd_e : 0.000525
  EX_zn2_e : 0.000525

Product: (mmol/gDw/h)
  EX_h2o_e : 24.557433
  EX_co2_e : 19.832888
  EX_h_e : 1.273463
  EX_acald_e : 0.424522
  Auxiliary production reaction : 0.137205
  DM_hmfurn_c : 0.000074

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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