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 : 12dgr140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3646 STM4482 STM1749 STM2463 STM2285 STM3526 STM3091 STM3512 STM3541 STM4326 STM1511 STM2952 STM0840 STM0842 STM1135 STM4183 STM0369 STM1448 STM3062 STM4484 STM2317 STM3179 STM1480 STM4126 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.207289 (mmol/gDw/h)
  Minimum Production Rate : 0.033818 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.284357
  EX_so4_e : 0.391373
  EX_pi_e : 0.183829
  EX_k_e : 0.036815
  EX_mg2_e : 0.001637
  EX_fe2_e : 0.001519
  EX_ca2_e : 0.000982
  EX_cl_e : 0.000982
  EX_cu2_e : 0.000655
  EX_mn2_e : 0.000655
  EX_mobd_e : 0.000655
  EX_zn2_e : 0.000655
  EX_cobalt2_e : 0.000655

Product: (mmol/gDw/h)
  EX_h2o_e : 25.608337
  EX_co2_e : 19.859903
  EX_h_e : 1.030329
  EX_acald_e : 0.528843
  EX_h2s_e : 0.366087
  Auxiliary production reaction : 0.033818
  EX_glyc__R_e : 0.005182
  DM_hmfurn_c : 0.000092

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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