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 : pg160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM2927 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM1884 STM2947 STM3709 STM1620 STM0974 STM1448 STM1326 STM4062 STM3069 STM0518 STM4184 STM4484 STM0542 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM1124 STM4467 STM2196 STM3240 STM2041 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.061361 (mmol/gDw/h)
  Minimum Production Rate : 0.055127 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.390121
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.676198
  EX_pi_e : 0.109542
  EX_k_e : 0.010898
  EX_so4_e : 0.007485
  EX_mg2_e : 0.000484
  EX_fe2_e : 0.000448
  EX_ca2_e : 0.000291
  EX_cl_e : 0.000291
  EX_cobalt2_e : 0.000194
  EX_cu2_e : 0.000194
  EX_mn2_e : 0.000194
  EX_mobd_e : 0.000194
  EX_zn2_e : 0.000194

Product: (mmol/gDw/h)
  EX_h2o_e : 12.102854
  EX_co2_e : 10.301006
  EX_dha_e : 4.938370
  EX_h_e : 0.468131
  EX_acald_e : 0.204678
  Auxiliary production reaction : 0.055127
  EX_glyclt_e : 0.003068
  DM_hmfurn_c : 0.000027

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
Contact