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 (20 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM0169 STM0861 STM4326 STM1511 STM2952 STM0321 STM2947 STM3709 STM1135 STM4183 STM0370 STM3597 STM1326 STM4062 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM0977 STM0007 STM2473 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.184374 (mmol/gDw/h)
  Minimum Production Rate : 0.061180 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.031823
  EX_pi_e : 0.224687
  EX_k_e : 0.032745
  EX_so4_e : 0.022490
  EX_mg2_e : 0.001456
  EX_fe2_e : 0.001351
  EX_cl_e : 0.000873
  EX_ca2_e : 0.000873
  EX_cobalt2_e : 0.000582
  EX_cu2_e : 0.000582
  EX_mn2_e : 0.000582
  EX_mobd_e : 0.000582
  EX_zn2_e : 0.000582

Product: (mmol/gDw/h)
  EX_h2o_e : 24.807571
  EX_co2_e : 19.602342
  EX_h_e : 1.501870
  EX_acald_e : 0.470380
  Auxiliary production reaction : 0.061180
  DM_hmfurn_c : 0.000082

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