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 (33 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM1463 STM4482 STM1749 STM2463 STM2285 STM3526 STM3512 STM3541 STM4326 STM2947 STM3068 STM2141 STM1620 STM0368 STM1448 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.192376 (mmol/gDw/h)
  Minimum Production Rate : 0.218314 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.120008
  EX_pi_e : 0.170603
  EX_k_e : 0.034166
  EX_so4_e : 0.023466
  EX_mg2_e : 0.001519
  EX_fe2_e : 0.001410
  EX_ca2_e : 0.000911
  EX_cl_e : 0.000911
  EX_cobalt2_e : 0.000608
  EX_cu2_e : 0.000608
  EX_mn2_e : 0.000608
  EX_mobd_e : 0.000608
  EX_zn2_e : 0.000608

Product: (mmol/gDw/h)
  EX_h2o_e : 24.914570
  EX_co2_e : 19.611095
  EX_h_e : 1.858822
  Auxiliary production reaction : 0.218314
  EX_acald_e : 0.154143
  EX_glyclt_e : 0.009619
  DM_hmfurn_c : 0.000086

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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