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 (100 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM3091 STM4326 STM1511 STM1884 STM2952 STM0321 STM1299 STM2947 STM3709 STM3068 STM2141 STM1620 STM0369 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM1933 STM3063 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.020648 (mmol/gDw/h)
  Minimum Production Rate : 0.060144 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.220678
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.275133
  EX_pi_e : 0.126045
  EX_k_e : 0.003667
  EX_so4_e : 0.002519
  EX_mg2_e : 0.000163
  EX_fe2_e : 0.000151
  EX_ca2_e : 0.000098
  EX_cl_e : 0.000098
  EX_cobalt2_e : 0.000065
  EX_cu2_e : 0.000065
  EX_mn2_e : 0.000065
  EX_mobd_e : 0.000065
  EX_zn2_e : 0.000065

Product: (mmol/gDw/h)
  EX_h2o_e : 11.499818
  EX_co2_e : 10.513517
  EX_dha_e : 4.899943
  EX_h_e : 0.211115
  Auxiliary production reaction : 0.060144
  EX_acald_e : 0.052678
  EX_lipa_e : 0.023795
  EX_glyclt_e : 0.001032

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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