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 : 1odec11eg3p_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: STM3646 STM0158 STM1463 STM1597 STM1749 STM2463 STM2285 STM3526 STM4570 STM4326 STM1299 STM2947 STM3709 STM1135 STM0141 STM1448 STM1326 STM4062 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3968 STM1124 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.272517 (mmol/gDw/h)
  Minimum Production Rate : 0.014046 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.383557
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.003177
  EX_pi_e : 0.255720
  EX_k_e : 0.048399
  EX_so4_e : 0.033242
  EX_mg2_e : 0.002152
  EX_fe3_e : 0.001997
  EX_ca2_e : 0.001291
  EX_cl_e : 0.001291
  EX_cu2_e : 0.000861
  EX_mn2_e : 0.000861
  EX_mobd_e : 0.000861
  EX_zn2_e : 0.000861
  EX_cobalt2_e : 0.000861

Product: (mmol/gDw/h)
  EX_h2o_e : 25.310146
  EX_co2_e : 17.770215
  EX_h_e : 2.312732
  EX_acald_e : 0.695254
  Auxiliary production reaction : 0.014046
  EX_hxa_e : 0.000437
  DM_hmfurn_c : 0.000122

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.

Last updated: 27-Sep-2023
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