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 : pa180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3646 STM2285 STM3526 STM4326 STM1511 STM1884 STM2952 STM0840 STM0842 STM1135 STM4183 STM0368 STM0974 STM1448 STM3062 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM1124 STM2196 STM3240 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.236931 (mmol/gDw/h)
  Minimum Production Rate : 0.042974 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.611007
  EX_pi_e : 0.253089
  EX_k_e : 0.042079
  EX_so4_e : 0.028901
  EX_mg2_e : 0.001871
  EX_fe2_e : 0.001736
  EX_ca2_e : 0.001122
  EX_cl_e : 0.001122
  EX_cobalt2_e : 0.000748
  EX_cu2_e : 0.000748
  EX_mn2_e : 0.000748
  EX_mobd_e : 0.000748
  EX_zn2_e : 0.000748

Product: (mmol/gDw/h)
  EX_h2o_e : 25.758872
  EX_co2_e : 19.141152
  EX_h_e : 2.014530
  Auxiliary production reaction : 0.042974
  EX_glyc__R_e : 0.005923
  DM_hmfurn_c : 0.000106

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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