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 : pe140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM4567 STM4326 STM0321 STM2947 STM3709 STM1570 STM1620 STM4036 STM0491 STM0368 STM1448 STM1326 STM4062 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277031 (mmol/gDw/h)
  Minimum Production Rate : 0.004955 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.331644
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.057872
  EX_pi_e : 0.250632
  EX_k_e : 0.049201
  EX_so4_e : 0.033793
  EX_mg2_e : 0.002187
  EX_fe2_e : 0.002030
  EX_ca2_e : 0.001312
  EX_cl_e : 0.001312
  EX_cobalt2_e : 0.000875
  EX_cu2_e : 0.000875
  EX_mn2_e : 0.000875
  EX_mobd_e : 0.000875
  EX_zn2_e : 0.000875

Product: (mmol/gDw/h)
  EX_h2o_e : 25.321181
  EX_co2_e : 17.669048
  EX_h_e : 2.357459
  EX_acald_e : 0.711724
  EX_glyclt_e : 0.013852
  Auxiliary production reaction : 0.004955
  DM_hmfurn_c : 0.000124

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