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 : 12dgr140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM0169 STM0861 STM4326 STM0321 STM2947 STM3709 STM3068 STM2141 STM1620 STM1448 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM3241 STM0973 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 : 0.269561 (mmol/gDw/h)
  Minimum Production Rate : 0.066069 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 15.033032
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.970602
  EX_pi_e : 0.239053
  EX_k_e : 0.047874
  EX_so4_e : 0.032882
  EX_mg2_e : 0.002128
  EX_fe2_e : 0.001976
  EX_ca2_e : 0.001277
  EX_cl_e : 0.001277
  EX_cobalt2_e : 0.000851
  EX_cu2_e : 0.000851
  EX_mn2_e : 0.000851
  EX_mobd_e : 0.000851
  EX_zn2_e : 0.000851

Product: (mmol/gDw/h)
  EX_h2o_e : 23.619534
  EX_co2_e : 16.122119
  EX_h_e : 2.298716
  EX_acald_e : 0.687713
  Auxiliary production reaction : 0.066069
  EX_glyclt_e : 0.013478
  DM_hmfurn_c : 0.000120

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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