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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM1749 STM2463 STM4108 STM2285 STM3526 STM0322 STM1290 STM4326 STM1884 STM2947 STM3529 STM1620 STM0491 STM0370 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM0402 STM0608 STM3708 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.240434 (mmol/gDw/h)
  Minimum Production Rate : 0.031804 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.649613
  EX_pi_e : 0.245027
  EX_k_e : 0.042701
  EX_so4_e : 0.029329
  EX_mg2_e : 0.001898
  EX_fe2_e : 0.001762
  EX_ca2_e : 0.001139
  EX_cl_e : 0.001139
  EX_cobalt2_e : 0.000759
  EX_cu2_e : 0.000759
  EX_mn2_e : 0.000759
  EX_mobd_e : 0.000759
  EX_zn2_e : 0.000759

Product: (mmol/gDw/h)
  EX_h2o_e : 25.741131
  EX_co2_e : 19.049171
  EX_h_e : 2.050328
  EX_acald_e : 0.192649
  Auxiliary production reaction : 0.031804
  EX_glyclt_e : 0.012022
  EX_glyald_e : 0.000167
  DM_hmfurn_c : 0.000107

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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