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 : pa120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM0158 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1885 STM2947 STM3709 STM1620 STM0491 STM1448 STM1326 STM4062 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.070256 (mmol/gDw/h)
  Minimum Production Rate : 0.078284 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.124269
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.774222
  EX_pi_e : 0.140587
  EX_k_e : 0.012477
  EX_so4_e : 0.008570
  EX_mg2_e : 0.000555
  EX_fe2_e : 0.000515
  EX_ca2_e : 0.000333
  EX_cl_e : 0.000333
  EX_cobalt2_e : 0.000222
  EX_cu2_e : 0.000222
  EX_mn2_e : 0.000222
  EX_mobd_e : 0.000222
  EX_zn2_e : 0.000222

Product: (mmol/gDw/h)
  EX_h2o_e : 12.108240
  EX_co2_e : 10.014858
  EX_dha_e : 4.929436
  EX_h_e : 0.599110
  EX_acald_e : 0.179237
  Auxiliary production reaction : 0.078284
  EX_glyclt_e : 0.003513
  DM_hmfurn_c : 0.000031

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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