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 : clpn160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM0158 STM2927 STM1749 STM2463 STM2285 STM3526 STM4326 STM1885 STM2952 STM0321 STM2947 STM1620 STM3597 STM1326 STM4062 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM4578 STM2338 STM2466 STM4467 STM3802 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.069286 (mmol/gDw/h)
  Minimum Production Rate : 0.028661 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.162764
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.763531
  EX_pi_e : 0.118765
  EX_k_e : 0.012305
  EX_so4_e : 0.008452
  EX_mg2_e : 0.000547
  EX_fe2_e : 0.000508
  EX_ca2_e : 0.000328
  EX_cl_e : 0.000328
  EX_cobalt2_e : 0.000219
  EX_cu2_e : 0.000219
  EX_mn2_e : 0.000219
  EX_mobd_e : 0.000219
  EX_zn2_e : 0.000219

Product: (mmol/gDw/h)
  EX_h2o_e : 12.129299
  EX_co2_e : 10.075923
  EX_dha_e : 4.930410
  EX_h_e : 0.533515
  EX_acald_e : 0.176762
  Auxiliary production reaction : 0.028661
  EX_glyclt_e : 0.003464
  DM_hmfurn_c : 0.000031

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