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 : 2odecg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM0322 STM4568 STM4570 STM4326 STM2952 STM1299 STM2947 STM3709 STM3068 STM2141 STM1135 STM1570 STM4036 STM0369 STM1448 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0977 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.253024 (mmol/gDw/h)
  Minimum Production Rate : 0.017654 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 17.650918
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.788356
  EX_pi_e : 0.242042
  EX_k_e : 0.044937
  EX_so4_e : 0.030864
  EX_mg2_e : 0.001998
  EX_fe2_e : 0.001854
  EX_cl_e : 0.001199
  EX_ca2_e : 0.001199
  EX_cobalt2_e : 0.000799
  EX_cu2_e : 0.000799
  EX_mn2_e : 0.000799
  EX_mobd_e : 0.000799
  EX_zn2_e : 0.000799

Product: (mmol/gDw/h)
  EX_h2o_e : 25.146706
  EX_co2_e : 18.153618
  EX_h_e : 2.127385
  EX_acald_e : 0.844005
  Auxiliary production reaction : 0.017654
  DM_hmfurn_c : 0.000113

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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