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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM2927 STM0051 STM1749 STM2463 STM4275 STM0661 STM0980 STM2009 STM4567 STM4109 STM4085 STM4415 STM1620 STM2167 STM0694 STM3045 STM0974 STM0152 STM3062 STM0150 STM0542 STM1211 STM2317 STM2338 STM2466 STM3968 STM0208 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.182055 (mmol/gDw/h)
  Minimum Production Rate : 0.202871 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 14.604605
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.349514
  EX_pi_e : 0.567194
  EX_k_e : 0.032333
  EX_so4_e : 0.022207
  EX_mg2_e : 0.001437
  EX_fe2_e : 0.001334
  EX_cl_e : 0.000862
  EX_ca2_e : 0.000862
  EX_cobalt2_e : 0.000575
  EX_cu2_e : 0.000575
  EX_mn2_e : 0.000575
  EX_mobd_e : 0.000575
  EX_zn2_e : 0.000575

Product: (mmol/gDw/h)
  EX_h2o_e : 23.241019
  EX_co2_e : 13.885342
  EX_h_e : 4.769335
  EX_ac_e : 2.279339
  Auxiliary production reaction : 0.202871
  EX_ade_e : 0.019748
  EX_thymd_e : 0.013634
  EX_glyclt_e : 0.009103
  DM_hmfurn_c : 0.000081

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