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 : pa140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM4567 STM4326 STM1884 STM2952 STM0321 STM2947 STM3709 STM3068 STM2141 STM1620 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3241 STM0973 STM0977 STM4467 STM3802 STM2196 STM3240 STM2041 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.071148 (mmol/gDw/h)
  Minimum Production Rate : 0.065812 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.159749
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.784056
  EX_pi_e : 0.128907
  EX_k_e : 0.012636
  EX_so4_e : 0.008679
  EX_mg2_e : 0.000562
  EX_fe2_e : 0.000520
  EX_ca2_e : 0.000337
  EX_cl_e : 0.000337
  EX_cobalt2_e : 0.000225
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000225
  EX_mobd_e : 0.000225
  EX_zn2_e : 0.000225

Product: (mmol/gDw/h)
  EX_h2o_e : 12.144917
  EX_co2_e : 10.051878
  EX_dha_e : 4.928539
  EX_h_e : 0.606721
  EX_acald_e : 0.181514
  Auxiliary production reaction : 0.065812
  EX_glyclt_e : 0.003557
  DM_hmfurn_c : 0.000032

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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