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 : pa120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (130 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM2122 STM4108 STM2285 STM3526 STM4570 STM4326 STM1511 STM1884 STM0321 STM0517 STM2947 STM3068 STM2141 STM1135 STM4183 STM3597 STM0974 STM4408 STM3062 STM1291 STM0772 STM4585 STM3704 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM4467 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.061537 (mmol/gDw/h)
  Minimum Production Rate : 0.077483 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.396182
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.680436
  EX_pi_e : 0.132055
  EX_k_e : 0.010929
  EX_so4_e : 0.007506
  EX_mg2_e : 0.000486
  EX_fe2_e : 0.000450
  EX_ca2_e : 0.000292
  EX_cl_e : 0.000292
  EX_cu2_e : 0.000194
  EX_mn2_e : 0.000194
  EX_mobd_e : 0.000194
  EX_zn2_e : 0.000194
  EX_cobalt2_e : 0.000194

Product: (mmol/gDw/h)
  EX_h2o_e : 12.149079
  EX_co2_e : 10.293067
  EX_dha_e : 4.938192
  EX_h_e : 0.527055
  EX_acald_e : 0.205726
  Auxiliary production reaction : 0.077483
  EX_glyclt_e : 0.003077
  EX_ade_e : 0.000458
  DM_hmfurn_c : 0.000027

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.

Last updated: 27-Sep-2023
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