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 : gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3009 STM2927 STM1749 STM2463 STM4275 STM3554 STM2009 STM4568 STM2460 STM0694 STM3045 STM0974 STM0152 STM2338 STM2466 STM2332 STM0208 STM3802 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.344710 (mmol/gDw/h)
  Minimum Production Rate : 0.283746 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 12.231544
  EX_nh4_e : 5.230314
  EX_glc__D_e : 5.000000
  EX_pi_e : 0.873190
  EX_k_e : 0.061220
  EX_so4_e : 0.042048
  EX_mg2_e : 0.002721
  EX_fe2_e : 0.002526
  EX_ca2_e : 0.001633
  EX_cl_e : 0.001633
  EX_cobalt2_e : 0.001089
  EX_cu2_e : 0.001089
  EX_mn2_e : 0.001089
  EX_mobd_e : 0.001089
  EX_zn2_e : 0.001089

Product: (mmol/gDw/h)
  EX_h2o_e : 24.496823
  EX_co2_e : 11.279389
  EX_h_e : 5.338147
  EX_ac_e : 1.268009
  Auxiliary production reaction : 0.283746
  EX_ade_e : 0.002567
  DM_hmfurn_c : 0.000154

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.

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Last updated: 27-Sep-2023
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