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 : ocdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 13: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM2285 STM3526 STM4326 STM1885 STM2952 STM2947 STM3709 STM1135 STM0369 STM1448 STM1326 STM4062 STM2403 STM0393 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM1933 STM1124 STM3063 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 : 0.024203 (mmol/gDw/h)
  Minimum Production Rate : 0.080760 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.239405
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.322504
  EX_pi_e : 0.077248
  EX_k_e : 0.004298
  EX_so4_e : 0.002952
  EX_mg2_e : 0.000191
  EX_fe2_e : 0.000177
  EX_cl_e : 0.000115
  EX_ca2_e : 0.000115
  EX_cu2_e : 0.000076
  EX_mn2_e : 0.000076
  EX_mobd_e : 0.000076
  EX_zn2_e : 0.000076
  EX_cobalt2_e : 0.000076

Product: (mmol/gDw/h)
  EX_h2o_e : 11.525304
  EX_co2_e : 10.495469
  EX_dha_e : 4.882716
  EX_h_e : 0.397513
  Auxiliary production reaction : 0.080760
  EX_acald_e : 0.061747
  EX_kdo2lipid4_e : 0.027892
  DM_hmfurn_c : 0.000011

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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