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 : ddca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM3526 STM0322 STM1290 STM4326 STM1511 STM1884 STM0840 STM0842 STM2947 STM3709 STM1135 STM0369 STM3597 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2332 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.240707 (mmol/gDw/h)
  Minimum Production Rate : 0.104273 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.652619
  EX_pi_e : 0.213464
  EX_k_e : 0.042749
  EX_so4_e : 0.029362
  EX_mg2_e : 0.001900
  EX_fe2_e : 0.001764
  EX_cl_e : 0.001140
  EX_ca2_e : 0.001140
  EX_cobalt2_e : 0.000760
  EX_cu2_e : 0.000760
  EX_mn2_e : 0.000760
  EX_mobd_e : 0.000760
  EX_zn2_e : 0.000760

Product: (mmol/gDw/h)
  EX_h2o_e : 25.687684
  EX_co2_e : 19.051813
  EX_h_e : 2.144892
  EX_acald_e : 0.192868
  Auxiliary production reaction : 0.104273
  DM_hmfurn_c : 0.000107

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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