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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM4108 STM2285 STM3526 STM0322 STM0169 STM0861 STM4326 STM3709 STM3068 STM2141 STM1620 STM1448 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3802 STM2196 STM3240 STM0007 STM2473 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.256147 (mmol/gDw/h)
  Minimum Production Rate : 0.004510 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.822772
  EX_pi_e : 0.236176
  EX_k_e : 0.045492
  EX_so4_e : 0.031245
  EX_mg2_e : 0.002022
  EX_fe2_e : 0.001877
  EX_ca2_e : 0.001213
  EX_cl_e : 0.001213
  EX_cobalt2_e : 0.000809
  EX_cu2_e : 0.000809
  EX_mn2_e : 0.000809
  EX_mobd_e : 0.000809
  EX_zn2_e : 0.000809

Product: (mmol/gDw/h)
  EX_h2o_e : 25.575098
  EX_co2_e : 18.500039
  EX_h_e : 2.868064
  EX_ac_e : 0.688252
  EX_glyclt_e : 0.012807
  Auxiliary production reaction : 0.004510
  DM_hmfurn_c : 0.000114

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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