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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 118: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3009 STM3747 STM2421 STM1749 STM2463 STM4275 STM2285 STM3526 STM4570 STM1511 STM1620 STM2167 STM0506 STM0974 STM0152 STM1211 STM2317 STM3179 STM4569 STM2338 STM2466 STM3885 STM3793 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826 STM3334   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.073680 (mmol/gDw/h)
  Minimum Production Rate : 0.057167 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 8.407429
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.097790
  EX_pi_e : 0.122507
  EX_k_e : 0.013085
  EX_so4_e : 0.008988
  EX_mg2_e : 0.000582
  EX_fe2_e : 0.000540
  EX_cl_e : 0.000349
  EX_ca2_e : 0.000349
  EX_cobalt2_e : 0.000233
  EX_cu2_e : 0.000233
  EX_mn2_e : 0.000233
  EX_mobd_e : 0.000233
  EX_zn2_e : 0.000233

Product: (mmol/gDw/h)
  EX_h2o_e : 11.016851
  EX_h_e : 9.739209
  EX_ac_e : 8.710730
  EX_co2_e : 8.430444
  EX_etoh_e : 0.245140
  Auxiliary production reaction : 0.057167
  EX_glyclt_e : 0.003684
  DM_hmfurn_c : 0.000033

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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