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 : phe__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM3646 STM0158 STM1463 STM1749 STM2463 STM2285 STM3526 STM1290 STM4326 STM0840 STM0842 STM2947 STM3709 STM1135 STM2081 STM0974 STM1448 STM0150 STM4184 STM4484 STM0568 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1937 STM1124 STM4467 STM3802 STM2196 STM3240 STM0007 STM2473 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.248702 (mmol/gDw/h)
  Minimum Production Rate : 0.170859 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 16.552227
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.991678
  EX_pi_e : 0.220555
  EX_k_e : 0.044169
  EX_so4_e : 0.030337
  EX_mg2_e : 0.001964
  EX_fe2_e : 0.001823
  EX_ca2_e : 0.001178
  EX_cl_e : 0.001178
  EX_cobalt2_e : 0.000785
  EX_cu2_e : 0.000785
  EX_mn2_e : 0.000785
  EX_mobd_e : 0.000785
  EX_zn2_e : 0.000785

Product: (mmol/gDw/h)
  EX_h2o_e : 24.882962
  EX_co2_e : 17.092288
  EX_h_e : 2.359349
  EX_acald_e : 0.634496
  Auxiliary production reaction : 0.170859
  EX_ile__L_e : 0.080089
  DM_hmfurn_c : 0.000111

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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