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 : ser__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM3646 STM0158 STM2285 STM3526 STM4326 STM3709 STM1135 STM1570 STM4036 STM2167 STM1448 STM4184 STM4484 STM0399 STM1211 STM2317 STM0935 STM3179 STM1480 STM4126 STM2338 STM2466 STM1378 STM1888 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 : 0.034943 (mmol/gDw/h)
  Minimum Production Rate : 0.109660 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_o2_e : 3.072138
  EX_nh4_e : 0.494738
  EX_pi_e : 0.030988
  EX_k_e : 0.006206
  EX_so4_e : 0.004262
  EX_mg2_e : 0.000276
  EX_fe2_e : 0.000256
  EX_ca2_e : 0.000166
  EX_cl_e : 0.000166
  EX_cu2_e : 0.000110
  EX_mn2_e : 0.000110
  EX_mobd_e : 0.000110
  EX_zn2_e : 0.000110
  EX_cobalt2_e : 0.000110

Product: (mmol/gDw/h)
  EX_co2_e : 11.436852
  EX_etoh_e : 8.429559
  EX_h2o_e : 4.080276
  EX_h_e : 0.417135
  EX_ser__L_e : 0.109660
  EX_ac_e : 0.010366
  EX_glyc__R_e : 0.000874
  DM_hmfurn_c : 0.000016

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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