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 (8 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM4567 STM4326 STM1299 STM2947 STM3709 STM1620 STM0368 STM1448 STM1326 STM4062 STM3069 STM0518 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.270774 (mmol/gDw/h)
  Minimum Production Rate : 0.040038 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.202567
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.983961
  EX_pi_e : 0.280166
  EX_k_e : 0.048089
  EX_so4_e : 0.033029
  EX_mg2_e : 0.002138
  EX_fe2_e : 0.001984
  EX_ca2_e : 0.001283
  EX_cl_e : 0.001283
  EX_cobalt2_e : 0.000855
  EX_cu2_e : 0.000855
  EX_mn2_e : 0.000855
  EX_mobd_e : 0.000855
  EX_zn2_e : 0.000855

Product: (mmol/gDw/h)
  EX_h2o_e : 25.205892
  EX_co2_e : 17.701089
  EX_h_e : 2.269016
  EX_acald_e : 0.478399
  Auxiliary production reaction : 0.040038
  EX_glyclt_e : 0.013539
  DM_hmfurn_c : 0.000121

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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