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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2285 STM3526 STM4568 STM4570 STM4326 STM1511 STM2952 STM3068 STM2141 STM1620 STM3542 STM4485 STM0370 STM1448 STM3062 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.236521 (mmol/gDw/h)
  Minimum Production Rate : 0.060201 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.606489
  EX_pi_e : 0.269953
  EX_k_e : 0.042006
  EX_so4_e : 0.028851
  EX_mg2_e : 0.001867
  EX_fe2_e : 0.001733
  EX_cl_e : 0.001120
  EX_ca2_e : 0.001120
  EX_cobalt2_e : 0.000747
  EX_cu2_e : 0.000747
  EX_mn2_e : 0.000747
  EX_mobd_e : 0.000747
  EX_zn2_e : 0.000747

Product: (mmol/gDw/h)
  EX_h2o_e : 25.702225
  EX_co2_e : 19.061352
  EX_h_e : 2.087125
  EX_ac_e : 0.070166
  Auxiliary production reaction : 0.060201
  EX_glyclt_e : 0.011826
  DM_hmfurn_c : 0.000105

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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