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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM4482 STM1749 STM2463 STM2285 STM3526 STM0322 STM4567 STM3512 STM3541 STM4326 STM2952 STM0840 STM0842 STM2947 STM3709 STM1620 STM0370 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM0977 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.238572 (mmol/gDw/h)
  Minimum Production Rate : 0.013513 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.629097
  EX_pi_e : 0.238598
  EX_k_e : 0.042370
  EX_so4_e : 0.029102
  EX_mg2_e : 0.001884
  EX_fe2_e : 0.001748
  EX_ca2_e : 0.001130
  EX_cl_e : 0.001130
  EX_cobalt2_e : 0.000753
  EX_cu2_e : 0.000753
  EX_mn2_e : 0.000753
  EX_mobd_e : 0.000753
  EX_zn2_e : 0.000753

Product: (mmol/gDw/h)
  EX_h2o_e : 25.580250
  EX_co2_e : 18.962682
  EX_h_e : 2.020940
  EX_acald_e : 0.608653
  Auxiliary production reaction : 0.013513
  EX_glyclt_e : 0.011929
  DM_hmfurn_c : 0.000106

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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