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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM3646 STM0158 STM2285 STM3526 STM4326 STM1511 STM1885 STM0840 STM0842 STM0517 STM2947 STM3709 STM1135 STM2081 STM4183 STM1448 STM3062 STM0772 STM4585 STM3704 STM4484 STM2317 STM3179 STM1480 STM4126 STM1124 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 : 0.240053 (mmol/gDw/h)
  Minimum Production Rate : 0.015982 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.810336
  EX_pi_e : 0.212885
  EX_k_e : 0.042633
  EX_so4_e : 0.029282
  EX_mg2_e : 0.001895
  EX_fe2_e : 0.001759
  EX_cl_e : 0.001137
  EX_ca2_e : 0.001137
  EX_cobalt2_e : 0.000758
  EX_cu2_e : 0.000758
  EX_mn2_e : 0.000758
  EX_mobd_e : 0.000758
  EX_zn2_e : 0.000758

Product: (mmol/gDw/h)
  EX_h2o_e : 26.168842
  EX_co2_e : 18.710418
  EX_h_e : 2.211999
  EX_tyr__L_e : 0.164917
  Auxiliary production reaction : 0.015982
  EX_glyclt_e : 0.012003
  DM_hmfurn_c : 0.000107

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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